diff -Nru htsjdk-2.22.0+dfsg/debian/changelog htsjdk-2.23.0+dfsg/debian/changelog
--- htsjdk-2.22.0+dfsg/debian/changelog	2020-05-29 11:08:17.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/changelog	2020-09-22 13:14:11.000000000 +0000
@@ -1,6 +1,25 @@
+htsjdk (2.23.0+dfsg-2) unstable; urgency=medium
+
+  * source-only upload 
+
+ -- Olivier Sallou <osallou@debian.org>  Tue, 22 Sep 2020 13:14:11 +0000
+
+htsjdk (2.23.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Remove trailing whitespace in debian/changelog (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 10 Sep 2020 17:20:43 +0200
+
 htsjdk (2.22.0+dfsg-1) unstable; urgency=medium
 
-  * New upstream release 
+  * New upstream release
 
  -- Olivier Sallou <osallou@debian.org>  Fri, 29 May 2020 11:08:17 +0000
 
diff -Nru htsjdk-2.22.0+dfsg/debian/compat htsjdk-2.23.0+dfsg/debian/compat
--- htsjdk-2.22.0+dfsg/debian/compat	2020-05-29 11:08:17.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/compat	1970-01-01 00:00:00.000000000 +0000
@@ -1 +0,0 @@
-12
diff -Nru htsjdk-2.22.0+dfsg/debian/control htsjdk-2.23.0+dfsg/debian/control
--- htsjdk-2.22.0+dfsg/debian/control	2020-05-29 11:08:17.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/control	2020-09-22 13:14:11.000000000 +0000
@@ -10,14 +10,14 @@
                javahelper,
                gradle-debian-helper,
                maven-repo-helper,
-               debhelper (>= 12~),
+               debhelper-compat (= 13),
                libcommons-jexl2-java,
                libcommons-logging-java,
                libjaxb-api-java,
                libjaxb-java,
                libsnappy-java,
                libcommons-compress-java,
-               libxz-java (>= 1.5),
+               libxz-java,
                libngs-java,
 # required for correct dependencies for -doc
                default-jdk-doc,
@@ -26,10 +26,11 @@
                junit4,
                libjimfs-java,
                scala-library
-Standards-Version: 4.3.0
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/htsjdk
 Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git
 Homepage: http://samtools.github.io/htsjdk/
+Rules-Requires-Root: no
 
 Package: libhtsjdk-java
 Architecture: all
diff -Nru htsjdk-2.22.0+dfsg/debian/libhtsjdk-java-doc.javadoc htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc.javadoc
--- htsjdk-2.22.0+dfsg/debian/libhtsjdk-java-doc.javadoc	2020-05-29 11:08:17.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc.javadoc	2020-09-22 13:14:11.000000000 +0000
@@ -1 +1 @@
-build/docs/javadoc	/usr/share/doc/libhtsjdk-java/api/
+build/docs/javadoc	usr/share/doc/libhtsjdk-java-doc/api/
diff -Nru htsjdk-2.22.0+dfsg/debian/patches/92-disable-testhttp.patch htsjdk-2.23.0+dfsg/debian/patches/92-disable-testhttp.patch
--- htsjdk-2.22.0+dfsg/debian/patches/92-disable-testhttp.patch	2020-05-29 11:08:17.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/patches/92-disable-testhttp.patch	2020-09-22 13:14:11.000000000 +0000
@@ -35,31 +35,6 @@
      @Test(dataProvider = "customInflaterInput", singleThreaded = true)
      public void testCustomInflater(final CheckedExceptionInputStreamSupplier bcisSupplier,
                                     final Supplier<List<String>> expectedOutputSupplier,
---- a/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java
-+++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java
-@@ -22,22 +22,6 @@
-         Assert.assertEquals(SeekableStreamFactory.isFilePath("ftp://broadinstitute.org"), false);
-     }
- 
--    @DataProvider(name="getStreamForData")
--    public Object[][] getStreamForData() throws Exception {
--        return new Object[][] {
--                { new File(TEST_DATA_DIR, "BAMFileIndexTest/index_test.bam").getAbsolutePath(),
--                        new File(TEST_DATA_DIR, "BAMFileIndexTest/index_test.bam").getAbsolutePath() },
--                { new File(TEST_DATA_DIR, "cram_with_bai_index.cram").getAbsolutePath(),
--                        new File(TEST_DATA_DIR, "cram_with_bai_index.cram").getAbsolutePath() },
--                { new URL("file://" + new File(TEST_DATA_DIR, "cram_with_bai_index.cram").getAbsolutePath()).toExternalForm(),
--                        new File(TEST_DATA_DIR, "cram_with_bai_index.cram").getAbsolutePath() },
--                { new URL(TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam").toExternalForm(),
--                        new URL(TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam").toExternalForm() },
--                { new URL(TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam.bai").toExternalForm(),
--                       new URL(TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam.bai").toExternalForm() }
--        };
--    }
--
-     @Test(dataProvider = "getStreamForData")
-     public void testGetStreamFor(final String path, final String expectedPath) throws IOException {
-         Assert.assertEquals(SeekableStreamFactory.getInstance().getStreamFor(path).getSource(), expectedPath);
 --- a/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
 +++ b/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
 @@ -230,66 +230,6 @@
diff -Nru htsjdk-2.22.0+dfsg/debian/salsa-ci.yml htsjdk-2.23.0+dfsg/debian/salsa-ci.yml
--- htsjdk-2.22.0+dfsg/debian/salsa-ci.yml	1970-01-01 00:00:00.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/salsa-ci.yml	2020-09-22 13:14:11.000000000 +0000
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
diff -Nru htsjdk-2.22.0+dfsg/debian/upstream/metadata htsjdk-2.23.0+dfsg/debian/upstream/metadata
--- htsjdk-2.22.0+dfsg/debian/upstream/metadata	1970-01-01 00:00:00.000000000 +0000
+++ htsjdk-2.23.0+dfsg/debian/upstream/metadata	2020-09-22 13:14:11.000000000 +0000
@@ -0,0 +1,5 @@
+---
+Bug-Database: https://github.com/samtools/htsjdk/issues
+Bug-Submit: https://github.com/samtools/htsjdk/issues/new
+Repository: https://github.com/samtools/htsjdk.git
+Repository-Browse: https://github.com/samtools/htsjdk
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/SAMReadGroupRecord.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMReadGroupRecord.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/SAMReadGroupRecord.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMReadGroupRecord.java	2020-07-08 16:28:01.000000000 +0000
@@ -27,7 +27,13 @@
 import htsjdk.samtools.util.Iso8601Date;
 import htsjdk.samtools.util.SamConstants;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * Header information about a read group.
@@ -53,13 +59,13 @@
 
     /* Platform values for the @RG-PL tag */
     public enum PlatformValue {
-        CAPILLARY, LS454, ILLUMINA,
+        BGI, CAPILLARY, LS454, ILLUMINA,
         SOLID, HELICOS, IONTORRENT, 
-        ONT, PACBIO
+        ONT, PACBIO, OTHER
     }
 
     public static final Set<String> STANDARD_TAGS =
-            new HashSet<String>(Arrays.asList(READ_GROUP_ID_TAG, SEQUENCING_CENTER_TAG, DESCRIPTION_TAG,
+            new HashSet<>(Arrays.asList(READ_GROUP_ID_TAG, SEQUENCING_CENTER_TAG, DESCRIPTION_TAG,
                     DATE_RUN_PRODUCED_TAG, FLOW_ORDER_TAG, KEY_SEQUENCE_TAG, LIBRARY_TAG,
                     PROGRAM_GROUP_TAG, PREDICTED_MEDIAN_INSERT_SIZE_TAG, PLATFORM_TAG, PLATFORM_MODEL_TAG,
                     PLATFORM_UNIT_TAG, READ_GROUP_SAMPLE_TAG, BARCODE_TAG));
@@ -121,8 +127,11 @@
 
     public Date getRunDate() {
         final String dt = getAttribute(DATE_RUN_PRODUCED_TAG);
-        if (dt == null) return null;
-        else return new Iso8601Date(dt);
+        if (dt == null) {
+            return null;
+        } else {
+            return new Iso8601Date(dt);
+        }
     }
 
     public String getFlowOrder() { return getAttribute(FLOW_ORDER_TAG); }
@@ -149,7 +158,9 @@
 
     public Integer getPredictedMedianInsertSize() {
         final String stringRep = getAttribute(PREDICTED_MEDIAN_INSERT_SIZE_TAG);
-        if (stringRep == null) return null;
+        if (stringRep == null) {
+            return null;
+        }
         return Integer.parseInt(stringRep); 
     }
     public void setPredictedMedianInsertSize(final Integer predictedMedianInsertSize) {
@@ -173,12 +184,18 @@
     @Override
     public boolean equals(final Object o) {
         if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
 
         final SAMReadGroupRecord that = (SAMReadGroupRecord) o;
 
-        if (!attributesEqual(that)) return false;
-        if (mReadGroupId != null ? !mReadGroupId.equals(that.mReadGroupId) : that.mReadGroupId != null) return false;
+        if (!attributesEqual(that)) {
+            return false;
+        }
+        if (mReadGroupId != null ? !mReadGroupId.equals(that.mReadGroupId) : that.mReadGroupId != null) {
+            return false;
+        }
 
         return true;
     }
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java	2020-07-08 16:28:01.000000000 +0000
@@ -26,6 +26,7 @@
 import htsjdk.samtools.util.IOUtil;
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
 import java.net.URL;
 import java.nio.channels.SeekableByteChannel;
 import java.util.function.Function;
@@ -96,7 +97,14 @@
             } else if (path.startsWith("ftp:")) {
                 return new SeekableFTPStream(new URL(path));
             } else if (path.startsWith("file:")) {
-                return new SeekableFileStream(new File(new URL(path).getPath()));
+                try {
+                    // convert to URI in order to obtain a decoded version of the path string suitable
+                    // for use with the File constructor
+                    final String decodedPath = new URI(path).getPath();
+                    return new SeekableFileStream(new File(decodedPath));
+                } catch (java.net.URISyntaxException e) {
+                    throw new IllegalArgumentException(String.format("The input string %s contains a URI scheme but is not a valid URI", path), e);
+                }
             } else if (IOUtil.hasScheme(path)) {
                 return new SeekablePathStream(IOUtil.getPath(path), wrapper);
             } else {
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java	2020-07-08 16:28:01.000000000 +0000
@@ -143,8 +143,9 @@
 
     protected void validateOffset(int offset, final byte[] array) {
         if (offset < 0 || offset >= array.length) {
-            throw new IllegalArgumentException("The requested position is not covered by this " + this.getClass().getSimpleName() +
-                    " object.");
+            throw new IllegalArgumentException("The requested position is not covered by this " + this.getClass().getSimpleName() + " object. "
+                    + "\n Offset = " + offset + " Array length = " + array.length
+                    + "\n Record is: " + getRecord().toString());
         }
     }
 }
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/util/EdgeReadIterator.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/EdgeReadIterator.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/samtools/util/EdgeReadIterator.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/EdgeReadIterator.java	2020-07-08 16:28:01.000000000 +0000
@@ -95,24 +95,33 @@
             // 1-based reference position that the current base aligns to
             final int refPos = alignmentBlock.getReferenceStart();
 
-            // 0-based offset from the aligned position of the first base in the read to the aligned position
-            // of the current base.
-            final int refOffset = refPos - rec.getAlignmentStart();
-            final int refOffsetEnd = refPos - rec.getAlignmentStart() + alignmentBlock.getLength();
+            if (accumulator.isEmpty()) {
+                accumulator.add(createLocusInfo(getReferenceSequence(rec.getReferenceIndex()), rec.getAlignmentStart()));
+            }
+
+            // The accumulator should always have LocusInfos that correspond to one consecutive segment of loci from one reference
+            // sequence. So
+            // accumulator.get(0).getPosition() + accumulator.size() == accumulator.get(accumulator.size()-1).getPosition()+1
+            final int accumulatorNextPosition = accumulator.get(0).getPosition() + accumulator.size();
 
+            if (accumulatorNextPosition != accumulator.get(accumulator.size() - 1).getPosition() + 1) {
+                throw new IllegalStateException("The accumulator has gotten into a funk. Cannot continue");
+            }
 
             // Ensure there are AbstractLocusInfos up to and including this position
-            for (int j = accumulator.size(); j <= refOffsetEnd; ++j) {
-                accumulator.add(createLocusInfo(getReferenceSequence(rec.getReferenceIndex()),
-                        rec.getAlignmentStart() + j));
+            for (int locusPos = accumulatorNextPosition; locusPos <= refPos + alignmentBlock.getLength(); ++locusPos) {
+                accumulator.add(createLocusInfo(getReferenceSequence(rec.getReferenceIndex()), locusPos));
             }
 
             /* Let's assume an alignment block starts in some locus. 
              * We put two records to the accumulator. The first one has the "begin" type which corresponds to the locus 
              * where the block starts. The second one has the "end" type which corresponds to the other locus where the block ends. 
             */
-            int refOffsetInterval = refOffset; // corresponds to the beginning of the alignment block 
-            int refOffsetEndInterval = refOffsetEnd;
+
+            // 0-based offset from the aligned position of the first base in the read to the aligned position
+            // of the current base.
+            int refOffsetInterval = refPos - rec.getAlignmentStart(); // corresponds to the beginning of the alignment block
+            int refOffsetEndInterval = refOffsetInterval + alignmentBlock.getLength();;
             int startShift = 0;
 
             // intersect intervals and alignment block
@@ -133,7 +142,7 @@
                     }
                     // if the alignment block ends out of an interval, shift the ending position
                     final int readEnd = refPos + alignmentBlock.getLength();
-                    if (refPos + alignmentBlock.getLength() > intervalEnd) {
+                    if (readEnd > intervalEnd) {
                         refOffsetEndInterval = refOffsetEndInterval - (readEnd - intervalEnd) + 1;
                     }
                 }
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3BaseData.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3BaseData.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3BaseData.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3BaseData.java	2020-07-08 16:28:01.000000000 +0000
@@ -2,39 +2,57 @@
 
 import htsjdk.tribble.annotation.Strand;
 
+import java.util.ArrayList;
 import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 
 public class Gff3BaseData {
     private static final String ID_ATTRIBUTE_KEY = "ID";
     private static final String NAME_ATTRIBUTE_KEY = "Name";
     private static final String ALIAS_ATTRIBUTE_KEY = "Alias";
-    final String contig;
-    final String source;
-    final String type;
-    final int start;
-    final int end;
-    final Strand strand;
-    final int phase;
-    final Map<String, String> attributes;
-    final String id;
-    final String name;
-    final String alias;
-
-    Gff3BaseData(final String contig, final String source, final String type,
-                 final int start, final int end, final Strand strand, final int phase,
-                 final Map<String, String> attributes) {
+    private final String contig;
+    private final String source;
+    private final String type;
+    private final int start;
+    private final int end;
+    private final double score;
+    private final Strand strand;
+    private final int phase;
+    private final Map<String, List<String>> attributes;
+    private final String id;
+    private final String name;
+    private final List<String> aliases;
+    private final int hashCode;
+
+    public Gff3BaseData(final String contig, final String source, final String type,
+                 final int start, final int end, final Double score, final Strand strand, final int phase,
+                 final Map<String, List<String>> attributes) {
         this.contig = contig;
         this.source = source;
         this.type = type;
         this.start = start;
         this.end = end;
+        this.score = score;
         this.phase = phase;
         this.strand = strand;
-        this.attributes = Collections.unmodifiableMap(attributes);
-        this.id = attributes.get(ID_ATTRIBUTE_KEY);
-        this.name = attributes.get(NAME_ATTRIBUTE_KEY);
-        this.alias = attributes.get(ALIAS_ATTRIBUTE_KEY);
+        this.attributes = copyAttributesSafely(attributes);
+        this.id = Gff3Codec.extractSingleAttribute(attributes.get(ID_ATTRIBUTE_KEY));
+        this.name = Gff3Codec.extractSingleAttribute(attributes.get(NAME_ATTRIBUTE_KEY));
+        this.aliases = attributes.getOrDefault(ALIAS_ATTRIBUTE_KEY, Collections.emptyList());
+        this.hashCode = computeHashCode();
+    }
+
+    private static Map<String, List<String>> copyAttributesSafely(final Map<String, List<String>> attributes) {
+        final Map<String, List<String>> modifiableDeepMap = new LinkedHashMap<>();
+
+        for (final Map.Entry<String, List<String>> entry : attributes.entrySet()) {
+            final List<String> unmodifiableDeepList = Collections.unmodifiableList(new ArrayList<>(entry.getValue()));
+            modifiableDeepMap.put(entry.getKey(), unmodifiableDeepList);
+        }
+
+        return Collections.unmodifiableMap(modifiableDeepMap);
     }
 
     @Override
@@ -47,57 +65,109 @@
         }
 
         final Gff3BaseData otherBaseData = (Gff3BaseData) other;
-        boolean ret = otherBaseData.contig.equals(contig) &&
-                otherBaseData.source.equals(source) &&
-                otherBaseData.type.equals(type) &&
-                otherBaseData.start == start &&
-                otherBaseData.end == end &&
-                otherBaseData.phase == phase &&
-                otherBaseData.strand.equals(strand) &&
-                otherBaseData.attributes.equals(attributes);
-        if (id == null) {
-            ret = ret && otherBaseData.id == null;
+        boolean ret = otherBaseData.getContig().equals(getContig()) &&
+                otherBaseData.getSource().equals(getSource()) &&
+                otherBaseData.getType().equals(getType()) &&
+                otherBaseData.getStart() == getStart() &&
+                otherBaseData.getEnd() == getEnd() &&
+                ((Double)otherBaseData.getScore()).equals(score) &&
+                otherBaseData.getPhase() == getPhase() &&
+                otherBaseData.getStrand().equals(getStrand()) &&
+                otherBaseData.getAttributes().equals(getAttributes());
+        if (getId() == null) {
+            ret = ret && otherBaseData.getId() == null;
         } else {
-            ret = ret && otherBaseData.id != null && otherBaseData.id.equals(id);
+            ret = ret && otherBaseData.getId() != null && otherBaseData.getId().equals(getId());
         }
 
-        if (name == null) {
-            ret = ret && otherBaseData.name == null;
+        if (getName() == null) {
+            ret = ret && otherBaseData.getName() == null;
         } else {
-            ret = ret && otherBaseData.name != null && otherBaseData.name.equals(name);
+            ret = ret && otherBaseData.getName() != null && otherBaseData.getName().equals(getName());
         }
 
-        if (alias == null) {
-            ret = ret && otherBaseData.alias == null;
-        } else {
-            ret = ret && otherBaseData.alias != null && otherBaseData.alias.equals(alias);
-        }
+        ret = ret && otherBaseData.getAliases().equals(getAliases());
 
         return ret;
     }
 
     @Override
     public int hashCode() {
-        int hash = contig.hashCode();
-        hash = 31 * hash + source.hashCode();
-        hash = 31 * hash + type.hashCode();
-        hash = 31 * hash + start;
-        hash = 31 * hash + end;
-        hash = 31 * hash + phase;
-        hash = 31 * hash + strand.hashCode();
-        hash = 31 * hash + attributes.hashCode();
-        if (id != null) {
-            hash = 31 * hash + id.hashCode();
-        }
+        return hashCode;
+    }
 
-        if (name != null) {
-            hash = 31 * hash + name.hashCode();
+    private int computeHashCode() {
+        int hash = getContig().hashCode();
+        hash = 31 * hash + getSource().hashCode();
+        hash = 31 * hash + getType().hashCode();
+        hash = 31 * hash + getStart();
+        hash = 31 * hash + getEnd();
+        hash = 31 * hash + Double.hashCode(getScore());
+        hash = 31 * hash + getPhase();
+        hash = 31 * hash + getStrand().hashCode();
+        hash = 31 * hash + getAttributes().hashCode();
+        if (getId() != null) {
+            hash = 31 * hash + getId().hashCode();
         }
 
-        if (alias != null) {
-            hash = 31 * hash + alias.hashCode();
+        if (getName() != null) {
+            hash = 31 * hash + getName().hashCode();
         }
 
+        hash = 31 * hash + aliases.hashCode();
+
         return hash;
     }
+
+    public String getContig() {
+        return contig;
+    }
+
+    public String getSource() {
+        return source;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public int getStart() {
+        return start;
+    }
+
+    public int getEnd() {
+        return end;
+    }
+
+    public double getScore() {
+        return score;
+    }
+
+    public Strand getStrand() {
+        return strand;
+    }
+
+    public int getPhase() {
+        return phase;
+    }
+
+    public Map<String, List<String>> getAttributes() {
+        return attributes;
+    }
+
+    public List<String> getAttribute(final String key) {
+        return attributes.getOrDefault(key, Collections.emptyList());
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public List<String> getAliases() {
+        return aliases;
+    }
 }
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Codec.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Codec.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Codec.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Codec.java	2020-07-08 16:28:01.000000000 +0000
@@ -9,7 +9,6 @@
 import htsjdk.tribble.AbstractFeatureCodec;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodecHeader;
-import htsjdk.tribble.SimpleFeature;
 import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.annotation.Strand;
 import htsjdk.tribble.index.tabix.TabixFormat;
@@ -17,13 +16,13 @@
 import htsjdk.tribble.util.ParsingUtils;
 
 
+
 import java.io.*;
 import java.net.URLDecoder;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.*;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
 
 /**
@@ -37,10 +36,7 @@
 
 public class Gff3Codec extends AbstractFeatureCodec<Gff3Feature, LineIterator> {
 
-    private static final char FIELD_DELIMITER = '\t';
-    private static final char ATTRIBUTE_DELIMITER = ';';
-    private static final char KEY_VALUE_SEPARATOR = '=';
-    private static final char VALUE_DELIMITER = ',';
+
 
     private static final int NUM_FIELDS = 9;
 
@@ -49,15 +45,12 @@
     private static final int FEATURE_TYPE_INDEX = 2;
     private static final int START_LOCATION_INDEX = 3;
     private static final int END_LOCATION_INDEX = 4;
+    private static final int SCORE_INDEX = 5;
     private static final int GENOMIC_STRAND_INDEX = 6;
     private static final int GENOMIC_PHASE_INDEX = 7;
     private static final int EXTRA_FIELDS_INDEX = 8;
 
-    private static final String COMMENT_START = "#";
 
-    private static final String DIRECTIVE_START = "##";
-
-    static final String PARENT_ATTRIBUTE_KEY = "Parent";
     private static final String IS_CIRCULAR_ATTRIBUTE_KEY = "Is_circular";
 
     private static final String ARTEMIS_FASTA_MARKER = ">";
@@ -67,20 +60,38 @@
     private final Map<String, Set<Gff3FeatureImpl>> activeFeaturesWithIDs = new HashMap<>();
     private final Map<String, Set<Gff3FeatureImpl>> activeParentIDs = new HashMap<>();
 
-    private int currentLineNum = 0;
-
-    private final Map<String, SequenceRegion> sequenceRegionMap = new HashMap<>();
+    private final Map<String, SequenceRegion> sequenceRegionMap = new LinkedHashMap<>();
+    private final Map<Integer, String> commentsWithLineNumbers = new LinkedHashMap<>();
 
     private final static Log logger = Log.getInstance(Gff3Codec.class);
 
     private boolean reachedFasta = false;
 
+    private DecodeDepth decodeDepth;
+
+    private int currentLine = 0;
+
     public Gff3Codec() {
+        this(DecodeDepth.DEEP);
+    }
+
+    public Gff3Codec(final DecodeDepth decodeDepth) {
         super(Gff3Feature.class);
+        this.decodeDepth = decodeDepth;
+    }
+
+    public enum DecodeDepth {
+        DEEP ,
+        SHALLOW
     }
 
     @Override
     public Gff3Feature decode(final LineIterator lineIterator) throws IOException {
+        return decode(lineIterator, decodeDepth);
+    }
+
+    private Gff3Feature decode(final LineIterator lineIterator, final DecodeDepth depth) throws IOException {
+        currentLine++;
         /*
         Basic strategy: Load features into deque, create maps from a features ID to it, and from a features parents' IDs to it.  For each feature, link to parents using these maps.
         When reaching flush directive, fasta, or end of file, prepare to flush features by moving all active features to deque of features to flush, and clearing
@@ -93,7 +104,6 @@
         }
 
         final String line = lineIterator.next();
-        currentLineNum++;
 
         if (reachedFasta) {
             //previously reached fasta, flush whatever is active
@@ -107,37 +117,23 @@
             return featuresToFlush.poll();
         }
 
-        if (line.startsWith(COMMENT_START) && !line.startsWith(DIRECTIVE_START)) {
+        if (line.startsWith(Gff3Constants.COMMENT_START) && !line.startsWith(Gff3Constants.DIRECTIVE_START)) {
+            commentsWithLineNumbers.put(currentLine, line.substring(Gff3Constants.COMMENT_START.length()));
             return featuresToFlush.poll();
         }
 
-        if (line.startsWith(DIRECTIVE_START)) {
+        if (line.startsWith(Gff3Constants.DIRECTIVE_START)) {
             parseDirective(line);
             return featuresToFlush.poll();
         }
 
-        final List<String> splitLine = ParsingUtils.split(line, FIELD_DELIMITER);
 
-        if (splitLine.size() != NUM_FIELDS) {
-            throw new TribbleException("Found an invalid number of columns in the given Gff3 file on line "
-                    + currentLineNum + " - Given: " + splitLine.size() + " Expected: " + NUM_FIELDS + " : " + line);
-        }
-
-        try {
-            final String contig = URLDecoder.decode(splitLine.get(CHROMOSOME_NAME_INDEX), "UTF-8");
-            final String source = URLDecoder.decode(splitLine.get(ANNOTATION_SOURCE_INDEX), "UTF-8");
-            final String type = URLDecoder.decode(splitLine.get(FEATURE_TYPE_INDEX), "UTF-8");
-            final int start = Integer.parseInt(splitLine.get(START_LOCATION_INDEX));
-            final int end = Integer.parseInt(splitLine.get(END_LOCATION_INDEX));
-            final int phase = splitLine.get(GENOMIC_PHASE_INDEX).equals(".")? -1 : Integer.parseInt(splitLine.get(GENOMIC_PHASE_INDEX));
-            final Strand strand = Strand.decode(splitLine.get(GENOMIC_STRAND_INDEX));
-            final Map<String, String> attributes = parseAttributes(splitLine.get(EXTRA_FIELDS_INDEX));
 
-            final String parentIDAttribute = attributes.get(PARENT_ATTRIBUTE_KEY);
-            final List<String> parentIDs = parentIDAttribute != null? ParsingUtils.split(parentIDAttribute, VALUE_DELIMITER) : new ArrayList<>();
-
-            final Gff3FeatureImpl thisFeature = new Gff3FeatureImpl(contig, source, type, start, end, strand, phase, attributes);
-            activeFeatures.add(thisFeature);
+        final Gff3FeatureImpl thisFeature = new Gff3FeatureImpl(parseLine(line, currentLine));
+        activeFeatures.add(thisFeature);
+        if (depth == DecodeDepth.DEEP) {
+            //link to parents/children/co-features
+            final List<String> parentIDs = thisFeature.getAttribute(Gff3Constants.PARENT_ATTRIBUTE_KEY);
             final String id = thisFeature.getID();
 
             for (final String parentID : parentIDs) {
@@ -171,11 +167,14 @@
                     child.addParent(thisFeature);
                 }
             }
-            validateFeature(thisFeature);
-            return featuresToFlush.poll();
-        } catch( final NumberFormatException ex ){
-            throw new TribbleException("Cannot read integer value for start/end position!", ex);
         }
+
+        validateFeature(thisFeature);
+        if (depth == DecodeDepth.SHALLOW) {
+            //flush all features immediatly
+            prepareToFlushFeatures();
+        }
+        return featuresToFlush.poll();
     }
 
 
@@ -185,19 +184,71 @@
      * @return map of keys to values for attributes of this feature
      * @throws UnsupportedEncodingException
      */
-    static private Map<String,String> parseAttributes(final String attributesString) throws UnsupportedEncodingException {
-        final Map<String, String> attributes = new LinkedHashMap<>();
-        final List<String> splitLine = ParsingUtils.split(attributesString,ATTRIBUTE_DELIMITER);
+    static private Map<String, List<String>> parseAttributes(final String attributesString) throws UnsupportedEncodingException {
+        if (attributesString.equals(Gff3Constants.UNDEFINED_FIELD_VALUE)) {
+            return Collections.emptyMap();
+        }
+        final Map<String, List<String>> attributes = new LinkedHashMap<>();
+        final List<String> splitLine = ParsingUtils.split(attributesString,Gff3Constants.ATTRIBUTE_DELIMITER);
         for(String attribute : splitLine) {
-            final List<String> key_value = ParsingUtils.split(attribute,KEY_VALUE_SEPARATOR);
-            if (key_value.size()<2) {
-                continue;
+            final List<String> key_value = ParsingUtils.split(attribute,Gff3Constants.KEY_VALUE_SEPARATOR);
+            if (key_value.size() != 2) {
+                throw new TribbleException("Attribute string " + attributesString + " is invalid");
             }
-            attributes.put(URLDecoder.decode(key_value.get(0).trim(), "UTF-8"), URLDecoder.decode(key_value.get(1).trim(), "UTF-8"));
+            attributes.put(URLDecoder.decode(key_value.get(0).trim(), "UTF-8"), decodeAttributeValue(key_value.get(1).trim()));
         }
         return attributes;
     }
 
+    static private Gff3BaseData parseLine(final String line, final int currentLine) {
+        final List<String> splitLine = ParsingUtils.split(line, Gff3Constants.FIELD_DELIMITER);
+
+        if (splitLine.size() != NUM_FIELDS) {
+            throw new TribbleException("Found an invalid number of columns in the given Gff3 file at line + " + currentLine + " - Given: " + splitLine.size() + " Expected: " + NUM_FIELDS + " : " + line);
+        }
+
+        try {
+            final String contig = URLDecoder.decode(splitLine.get(CHROMOSOME_NAME_INDEX), "UTF-8");
+            final String source = URLDecoder.decode(splitLine.get(ANNOTATION_SOURCE_INDEX), "UTF-8");
+            final String type = URLDecoder.decode(splitLine.get(FEATURE_TYPE_INDEX), "UTF-8");
+            final int start = Integer.parseInt(splitLine.get(START_LOCATION_INDEX));
+            final int end = Integer.parseInt(splitLine.get(END_LOCATION_INDEX));
+            final double score = splitLine.get(SCORE_INDEX).equals(Gff3Constants.UNDEFINED_FIELD_VALUE) ? -1 : Double.parseDouble(splitLine.get(SCORE_INDEX));
+            final int phase = splitLine.get(GENOMIC_PHASE_INDEX).equals(Gff3Constants.UNDEFINED_FIELD_VALUE) ? -1 : Integer.parseInt(splitLine.get(GENOMIC_PHASE_INDEX));
+            final Strand strand = Strand.decode(splitLine.get(GENOMIC_STRAND_INDEX));
+            final Map<String, List<String>> attributes = parseAttributes(splitLine.get(EXTRA_FIELDS_INDEX));
+            return new Gff3BaseData(contig, source, type, start, end, score, strand, phase, attributes);
+        } catch (final NumberFormatException ex ) {
+            throw new TribbleException("Cannot read integer value for start/end position from line " + currentLine + ".  Line is: " + line, ex);
+        } catch (final IOException ex) {
+            throw new TribbleException("Cannot decode feature info from line " + currentLine + ".  Line is: " + line, ex);
+        }
+    }
+
+    /**
+     * Get list of sequence regions parsed by the codec.
+     * @return list of sequence regions
+     */
+    public List<SequenceRegion> getSequenceRegions() {
+        return Collections.unmodifiableList(new ArrayList<>(sequenceRegionMap.values()));
+    }
+
+    /**
+     * Gets map from line number to comment found on that line.  The text of the comment EXCLUDES the leading # which indicates a comment line.
+     * @return Map from line number to comment found on line
+     */
+    public Map<Integer, String> getCommentsWithLineNumbers() {
+        return Collections.unmodifiableMap(new LinkedHashMap<>(commentsWithLineNumbers));
+    }
+
+    /**
+     * Gets list of comments parsed by the codec.  Excludes leading # which indicates a comment line.
+     * @return
+     */
+    public List<String> getCommentTexts() {
+        return Collections.unmodifiableList(new ArrayList<>(commentsWithLineNumbers.values()));
+    }
+
     /**
      * If sequence region of feature's contig has been specified with sequence region directive, validates that
      * feature's coordinates are within the specified sequence region.  TribbleException is thrown if invalid.
@@ -208,7 +259,7 @@
             final SequenceRegion region = sequenceRegionMap.get(feature.getContig());
             if (feature.getStart() == region.getStart() && feature.getEnd() == region.getEnd()) {
                 //landmark feature
-                final boolean isCircular = Boolean.parseBoolean(feature.getAttribute(IS_CIRCULAR_ATTRIBUTE_KEY));
+                final boolean isCircular = Boolean.parseBoolean(extractSingleAttribute(feature.getAttribute(IS_CIRCULAR_ATTRIBUTE_KEY)));
                 region.setCircular(isCircular);
             }
             if (region.isCircular()? !region.overlaps(feature) : !region.contains(feature)) {
@@ -219,20 +270,8 @@
     }
 
     @Override
-    public Feature decodeLoc(LineIterator lineIterator) {
-        final String line = lineIterator.next();
-
-        if (line.startsWith(COMMENT_START)) {
-            return null;
-        }
-
-        final List<String> splitLine = ParsingUtils.split(line,FIELD_DELIMITER);
-
-        try {
-            return new SimpleFeature(splitLine.get(CHROMOSOME_NAME_INDEX), Integer.parseInt(splitLine.get(START_LOCATION_INDEX)), Integer.parseInt(splitLine.get(END_LOCATION_INDEX)));
-        } catch (final NumberFormatException ex ) {
-            throw new TribbleException("Cannot read integer value for start/end position!", ex);
-        }
+    public Feature decodeLoc(LineIterator lineIterator) throws IOException {
+        return decode(lineIterator, DecodeDepth.SHALLOW);
     }
 
     @Override
@@ -256,7 +295,7 @@
                     if (Gff3Directive.toDirective(line) != Gff3Directive.VERSION3_DIRECTIVE) {
                         return false;
                     }
-                    while (line.startsWith(COMMENT_START)) {
+                    while (line.startsWith(Gff3Constants.COMMENT_START)) {
                         line = br.readLine();
                         if ( line == null ) {
                             return false;
@@ -264,7 +303,7 @@
                     }
 
                     // make sure line conforms to gtf spec
-                    final List<String> fields = ParsingUtils.split(line,FIELD_DELIMITER);
+                    final List<String> fields = ParsingUtils.split(line, Gff3Constants.FIELD_DELIMITER);
 
                     canDecode &= fields.size() == NUM_FIELDS;
 
@@ -300,13 +339,40 @@
         return canDecode;
     }
 
+    static List<String> decodeAttributeValue(final String attributeValue) {
+        //split on VALUE_DELIMITER, then decode
+        final List<String> splitValues = ParsingUtils.split(attributeValue, Gff3Constants.VALUE_DELIMITER);
+
+        final List<String> decodedValues = new ArrayList<>();
+        for (final String encodedValue : splitValues) {
+            try {
+                decodedValues.add(URLDecoder.decode(encodedValue.trim(), "UTF-8"));
+            } catch (final UnsupportedEncodingException ex) {
+                throw new TribbleException("Error decoding attribute " + encodedValue, ex);
+            }
+        }
+
+        return decodedValues;
+    }
+
+    static String extractSingleAttribute(final List<String> values) {
+        if (values == null || values.isEmpty()) {
+            return null;
+        }
+
+        if (values.size() != 1) {
+            throw new TribbleException("Attribute has multiple values when only one expected");
+        }
+        return values.get(0);
+    }
+
     @Override
     public FeatureCodecHeader readHeader(LineIterator lineIterator) {
 
         List<String> header = new ArrayList<>();
         while(lineIterator.hasNext()) {
             String line = lineIterator.peek();
-            if (line.startsWith(COMMENT_START)) {
+            if (line.startsWith(Gff3Constants.COMMENT_START)) {
                 header.add(line);
                 lineIterator.next();
             } else {
@@ -407,29 +473,75 @@
     /**
      * Enum for parsing directive lines.  If information in directive line needs to be parsed beyond specifying directive type, decode method should be overriden
      */
-    enum Gff3Directive {
+    public enum Gff3Directive {
 
-        VERSION3_DIRECTIVE("##gff-version\\s+3(?:.\\d)*(?:\\.\\d)*$"),
+        VERSION3_DIRECTIVE("##gff-version\\s+3(?:\\.\\d*)*$") {
+            @Override
+             protected Object decode(final String line) throws IOException {
+                final String[] splitLine = line.split("\\s+");
+                return splitLine[1];
+            }
+
+            @Override
+            String encode(final Object object) {
+                if (object == null) {
+                    throw new TribbleException("Cannot encode null in VERSION3_DIRECTIVE");
+                }
+                if (!(object instanceof String)) {
+                    throw new TribbleException("Cannot encode object of type " + object.getClass() + " in VERSION3_DIRECTIVE");
+                }
+
+                final String versionLine = "##gff-version " + (String)object;
+                if (!regexPattern.matcher(versionLine).matches()) {
+                    throw new TribbleException("Version " + (String)object + " is not a valid version");
+                }
+
+                return versionLine;
+            }
+        },
 
         SEQUENCE_REGION_DIRECTIVE("##sequence-region\\s+.+ \\d+ \\d+$") {
-            private int CONTIG_INDEX = 1;
-            private int START_INDEX = 2;
-            private int END_INDEX = 3;
+            final private int CONTIG_INDEX = 1;
+            final private int START_INDEX = 2;
+            final private int END_INDEX = 3;
             @Override
-            public Object decode(final String line) throws IOException {
+            protected Object decode(final String line) throws IOException {
                 final String[] splitLine = line.split("\\s+");
                 final String contig = URLDecoder.decode(splitLine[CONTIG_INDEX], "UTF-8");
                 final int start = Integer.parseInt(splitLine[START_INDEX]);
                 final int end = Integer.parseInt(splitLine[END_INDEX]);
                 return new SequenceRegion(contig, start, end);
             }
+
+            @Override
+            String encode(final Object object) {
+                if (object == null) {
+                    throw new TribbleException("Cannot encode null in SEQUENCE_REGION_DIRECTIVE");
+                }
+                if (!(object instanceof SequenceRegion)) {
+                    throw new TribbleException("Cannot encode object of type " + object.getClass() + " in SEQUENCE_REGION_DIRECTIVE");
+                }
+
+                final SequenceRegion sequenceRegion = (SequenceRegion) object;
+                return "##sequence-region " + Gff3Writer.encodeString(sequenceRegion.getContig()) + " " + sequenceRegion.getStart() + " " + sequenceRegion.getEnd();
+            }
         },
 
-        FLUSH_DIRECTIVE("###$"),
+        FLUSH_DIRECTIVE("###$") {
+            @Override
+            String encode(final Object object) {
+                return "###";
+            }
+        },
 
-        FASTA_DIRECTIVE("##FASTA$");
+        FASTA_DIRECTIVE("##FASTA$") {
+            @Override
+            String encode(final Object object) {
+                return "##FASTA";
+            }
+        };
 
-        private final Pattern regexPattern;
+        protected final Pattern regexPattern;
 
         Gff3Directive(String regex) {
             this.regexPattern = Pattern.compile(regex);
@@ -444,9 +556,11 @@
             return null;
         }
 
-        public Object decode(final String line) throws IOException {
+        protected Object decode(final String line) throws IOException {
             return null;
         }
+
+        abstract String encode(final Object object);
     }
 
 }
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Constants.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Constants.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Constants.java	1970-01-01 00:00:00.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Constants.java	2020-07-08 16:28:01.000000000 +0000
@@ -0,0 +1,13 @@
+package htsjdk.tribble.gff;
+
+public class Gff3Constants {
+     public static final char FIELD_DELIMITER = '\t';
+     public static final char ATTRIBUTE_DELIMITER = ';';
+     public static final char KEY_VALUE_SEPARATOR = '=';
+     public static final char VALUE_DELIMITER = ',';
+     public static final String COMMENT_START = "#";
+     public static final String DIRECTIVE_START = "##";
+     public static final String UNDEFINED_FIELD_VALUE = ".";
+     public static final String PARENT_ATTRIBUTE_KEY = "Parent";
+     public final static char END_OF_LINE_CHARACTER = '\n';
+}
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java	2020-07-08 16:28:01.000000000 +0000
@@ -30,12 +30,16 @@
     private final Set<Gff3FeatureImpl> topLevelFeatures = new HashSet<>();
 
     public Gff3FeatureImpl(final String contig, final String source, final String type,
-                           final int start, final int end, final Strand strand, final int phase,
-                           final Map<String, String> attributes) {
-        baseData = new Gff3BaseData(contig, source, type, start, end, strand, phase, attributes);
+                           final int start, final int end, final Double score, final Strand strand, final int phase,
+                           final Map<String, List<String>> attributes) {
+        baseData = new Gff3BaseData(contig, source, type, start, end, score, strand, phase, attributes);
 
     }
 
+    public Gff3FeatureImpl(final Gff3BaseData baseData) {
+        this.baseData = baseData;
+    }
+
     /**
      * Get the set of top level features from which this feature is descended
      * @return set of top level feature from which this feature is descended
@@ -80,15 +84,15 @@
     public Set<Gff3FeatureImpl> getAncestors() {
         final List<Gff3FeatureImpl> ancestors = new ArrayList<>(parents);
         for (final Gff3FeatureImpl parent : parents) {
-            ancestors.addAll(baseData.attributes.containsKey(DERIVES_FROM_ATTRIBUTE_KEY)? parent.getAncestors(baseData.attributes.get(DERIVES_FROM_ATTRIBUTE_KEY)) : parent.getAncestors());
+            ancestors.addAll(getAttribute(DERIVES_FROM_ATTRIBUTE_KEY).isEmpty()? parent.getAncestors() : parent.getAncestors(new HashSet<>(baseData.getAttributes().get(DERIVES_FROM_ATTRIBUTE_KEY))));
         }
         return new LinkedHashSet<>(ancestors);
     }
 
-    private Set<Gff3FeatureImpl> getAncestors(final String derivingFrom) {
+    private Set<Gff3FeatureImpl> getAncestors(final Collection<String> derivingFrom) {
         final List<Gff3FeatureImpl> ancestors = new ArrayList<>();
         for (final Gff3FeatureImpl parent : parents) {
-            if (parent.getID().equals(derivingFrom) || parent.getAncestors().stream().anyMatch(f -> f.getID().equals(derivingFrom))) {
+            if (derivingFrom.contains(parent.getID()) || parent.getAncestors().stream().anyMatch(f -> derivingFrom.contains(f.getID()))) {
                 ancestors.add(parent);
                 ancestors.addAll(parent.getAncestors());
             }
@@ -103,7 +107,7 @@
     @Override
     public Set<Gff3FeatureImpl> getDescendents() {
         final List<Gff3FeatureImpl> descendants = new ArrayList<>(children);
-        final Set<String> idsInLineage = new HashSet<>(Collections.singleton(baseData.id));
+        final Set<String> idsInLineage = new HashSet<>(Collections.singleton(baseData.getId()));
         idsInLineage.addAll(children.stream().map(Gff3Feature::getID).collect(Collectors.toSet()));
         for(final Gff3FeatureImpl child : children) {
             descendants.addAll(child.getDescendents(idsInLineage));
@@ -112,8 +116,8 @@
     }
 
     private Set<Gff3FeatureImpl> getDescendents(final Set<String> idsInLineage) {
-        final List<Gff3FeatureImpl> childrenToAdd = children.stream().filter(c -> c.getAttribute(DERIVES_FROM_ATTRIBUTE_KEY) == null ||
-                idsInLineage.contains(c.getAttribute(DERIVES_FROM_ATTRIBUTE_KEY))).
+        final List<Gff3FeatureImpl> childrenToAdd = children.stream().filter(c -> c.getAttribute(DERIVES_FROM_ATTRIBUTE_KEY).isEmpty() ||
+                !Collections.disjoint(idsInLineage, c.getAttribute(DERIVES_FROM_ATTRIBUTE_KEY))).
                 collect(Collectors.toList());
         final List<Gff3FeatureImpl> descendants = new ArrayList<>(childrenToAdd);
 
@@ -144,8 +148,8 @@
 
     public void addParent(final Gff3FeatureImpl parent) {
         final Set<Gff3FeatureImpl> topLevelFeaturesToAdd = new HashSet<>(parent.getTopLevelFeatures());
-        if (baseData.attributes.containsKey(DERIVES_FROM_ATTRIBUTE_KEY)) {
-            topLevelFeaturesToAdd.removeIf(f -> !f.getID().equals(baseData.attributes.get(DERIVES_FROM_ATTRIBUTE_KEY)) && f.getDescendents().stream().noneMatch(f2 -> f2.getID()== null? false:f2.getID().equals(baseData.attributes.get(DERIVES_FROM_ATTRIBUTE_KEY))));
+        if (!getAttribute(DERIVES_FROM_ATTRIBUTE_KEY).isEmpty()) {
+            topLevelFeaturesToAdd.removeIf(f -> !getAttribute(DERIVES_FROM_ATTRIBUTE_KEY).contains(f.getID()) && f.getDescendents().stream().noneMatch(f2 -> f2.getID()!= null && getAttribute(DERIVES_FROM_ATTRIBUTE_KEY).contains(f2.getID())));
         }
         parents.add(parent);
         parent.addChild(this);
@@ -184,7 +188,7 @@
     public void addCoFeature(final Gff3FeatureImpl coFeature) {
         if (!parents.equals(coFeature.getParents())) {
 
-            throw new TribbleException("Co-features " + baseData.id + " do not have same parents");
+            throw new TribbleException("Co-features " + baseData.getId() + " do not have same parents");
         }
         for (final Gff3FeatureImpl feature : coFeatures) {
             feature.addCoFeatureShallow(coFeature);
@@ -196,8 +200,8 @@
 
     private void addCoFeatureShallow(final Gff3FeatureImpl coFeature) {
         coFeatures.add(coFeature);
-        if (!coFeature.getID().equals(baseData.id)) {
-            throw new TribbleException("Attempting to add co-feature with id " + coFeature.getID() + " to feature with id " + baseData.id);
+        if (!coFeature.getID().equals(baseData.getId())) {
+            throw new TribbleException("Attempting to add co-feature with id " + coFeature.getID() + " to feature with id " + baseData.getId());
         }
     }
 
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Feature.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Feature.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Feature.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Feature.java	2020-07-08 16:28:01.000000000 +0000
@@ -23,45 +23,48 @@
 
 
     default String getSource() {
-        return getBaseData().source;
+        return getBaseData().getSource();
     }
 
     @Override
     default int getEnd() {
-        return getBaseData().end;
+        return getBaseData().getEnd();
     }
 
     default Strand getStrand() {
-        return getBaseData().strand;
+        return getBaseData().getStrand();
     }
 
     default int getPhase() {
-        return getBaseData().phase;
+        return getBaseData().getPhase();
     }
 
-    default String getType() {return getBaseData().type;}
+    default String getType() {return getBaseData().getType();}
 
     @Override
     default String getContig() {
-        return getBaseData().contig;
+        return getBaseData().getContig();
     }
 
      @Override
     default int getStart() {
-        return getBaseData().start;
+        return getBaseData().getStart();
     }
 
-    default String getAttribute(final String key) {
-        return getBaseData().attributes.get(key);
+
+    default List<String> getAttribute(final String key) {
+        return getBaseData().getAttribute(key);
     }
 
-    default Map<String, String> getAttributes() { return getBaseData().attributes;}
+    default Map<String, List<String>> getAttributes() { return getBaseData().getAttributes();}
+
+    default String getID() { return getBaseData().getId();}
 
-    default String getID() { return getBaseData().id;}
+    default String getName() { return getBaseData().getName();}
 
-    default String getName() { return getBaseData().name;}
+    default List<String> getAliases() { return getBaseData().getAliases();}
 
-    default String getAlias() { return getBaseData().alias;}
+    default double getScore() { return getBaseData().getScore();}
 
     /**
      * Get BaseData object which contains all the basic information of the feature
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Writer.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Writer.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Writer.java	1970-01-01 00:00:00.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/Gff3Writer.java	2020-07-08 16:28:01.000000000 +0000
@@ -0,0 +1,175 @@
+package htsjdk.tribble.gff;
+
+import htsjdk.samtools.util.BlockCompressedOutputStream;
+import htsjdk.samtools.util.FileExtensions;
+import htsjdk.samtools.util.IOUtil;
+import htsjdk.tribble.TribbleException;
+
+import java.io.BufferedOutputStream;
+import java.io.Closeable;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Consumer;
+
+
+/**
+ * A class to write out gff3 files.  Features are added using {@link #addFeature(Gff3Feature)}, directives using {@link #addDirective(Gff3Codec.Gff3Directive)},
+ * and comments using {@link #addComment(String)}.  Note that the version 3 directive is automatically added at creation, so should not be added separately.
+ */
+public class Gff3Writer implements Closeable {
+
+    private final OutputStream out;
+    private final static String version = "3.1.25";
+
+    public Gff3Writer(final Path path) throws IOException {
+        if (FileExtensions.GFF3.stream().noneMatch(e -> path.toString().endsWith(e))) {
+            throw new TribbleException("File " + path + " does not have extension consistent with gff3");
+        }
+
+        final OutputStream outputStream = IOUtil.hasGzipFileExtension(path)? new BlockCompressedOutputStream(path.toFile()) : Files.newOutputStream(path);
+        out = new BufferedOutputStream(outputStream);
+        //start with version directive
+        initialize();
+    }
+
+    public Gff3Writer(final OutputStream stream) {
+        out = stream;
+        initialize();
+    }
+
+    private void initialize() {
+        try {
+            writeWithNewLine(Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE.encode(version));
+        } catch (final IOException ex) {
+            throw new TribbleException("Error writing version directive", ex);
+        }
+    }
+
+    private void writeWithNewLine(final String txt) throws IOException {
+        out.write(txt.getBytes());
+        out.write(Gff3Constants.END_OF_LINE_CHARACTER);
+    }
+
+    private void tryToWrite(final String string) {
+        try {
+            out.write(string.getBytes());
+        } catch (final IOException ex) {
+            throw new TribbleException("Error writing out string " + string, ex);
+        }
+    }
+
+    private void writeFirstEightFields(final Gff3Feature feature) throws IOException {
+        writeJoinedByDelimiter(Gff3Constants.FIELD_DELIMITER, this::tryToWrite, Arrays.asList(
+                encodeString(feature.getContig()),
+                encodeString(feature.getSource()),
+                encodeString(feature.getType()),
+                Integer.toString(feature.getStart()),
+                Integer.toString(feature.getEnd()),
+                feature.getScore() < 0 ? Gff3Constants.UNDEFINED_FIELD_VALUE : Double.toString(feature.getScore()),
+                feature.getStrand().toString(),
+                feature.getPhase() < 0 ? Gff3Constants.UNDEFINED_FIELD_VALUE : Integer.toString(feature.getPhase())
+                )
+        );
+    }
+
+    void writeAttributes(final Map<String, List<String>> attributes) throws IOException {
+        if (attributes.isEmpty()) {
+            out.write(Gff3Constants.UNDEFINED_FIELD_VALUE.getBytes());
+        }
+
+        writeJoinedByDelimiter(Gff3Constants.ATTRIBUTE_DELIMITER, e ->  writeKeyValuePair(e.getKey(), e.getValue()), attributes.entrySet());
+    }
+
+    void writeKeyValuePair(final String key, final List<String> values) {
+        try {
+            tryToWrite(key);
+            out.write(Gff3Constants.KEY_VALUE_SEPARATOR);
+            writeJoinedByDelimiter(Gff3Constants.VALUE_DELIMITER, v -> tryToWrite(encodeString(v)), values);
+        } catch (final IOException ex) {
+            throw new TribbleException("error writing out key value pair " + key + " " + values);
+        }
+    }
+
+    private <T> void writeJoinedByDelimiter(final char delimiter, final Consumer<T> consumer, final Collection<T> fields) throws IOException {
+        boolean isNotFirstField = false;
+        for (final T field : fields) {
+            if (isNotFirstField) {
+                out.write(delimiter);
+            } else {
+                isNotFirstField = true;
+            }
+
+            consumer.accept(field);
+        }
+    }
+
+    /***
+     * add a feature
+     * @param feature the feature to be added
+     * @throws IOException
+     */
+    public void addFeature(final Gff3Feature feature) throws IOException {
+        writeFirstEightFields(feature);
+        out.write(Gff3Constants.FIELD_DELIMITER);
+        writeAttributes(feature.getAttributes());
+        out.write(Gff3Constants.END_OF_LINE_CHARACTER);
+    }
+
+    static String encodeString(final String s) {
+        try {
+            //URLEncoder.encode is hardcoded to change all spaces to +, but we want spaces left unchanged so have to do this
+            //+ is escaped to %2B, so no loss of information
+            return URLEncoder.encode(s, "UTF-8").replace("+", " ");
+        } catch (final UnsupportedEncodingException ex) {
+            throw new TribbleException("Encoding failure", ex);
+        }
+    }
+
+    /**
+     * Add a directive with an object
+     * @param directive the directive to be added
+     * @param object the object to be encoded with the directive
+     * @throws IOException
+     */
+    public void addDirective(final Gff3Codec.Gff3Directive directive, final Object object) throws IOException {
+        if (directive == Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE) {
+            throw new TribbleException("VERSION3_DIRECTIVE is automatically added and should not be added manually.");
+        }
+        writeWithNewLine(directive.encode(object));
+    }
+
+    /**
+     * Add a directive
+     * @param directive the directive to be added
+     * @throws IOException
+     */
+    public void addDirective(final Gff3Codec.Gff3Directive directive) throws IOException {
+        if (directive == Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE) {
+            throw new TribbleException("VERSION3_DIRECTIVE is automatically added and should not be added manually.");
+        }
+        addDirective(directive, null);
+    }
+
+    /**
+     * Add comment line
+     * @param comment the comment line (not including leading #)
+     * @throws IOException
+     */
+    public void addComment(final String comment) throws IOException {
+        out.write(Gff3Constants.COMMENT_START.getBytes());
+        writeWithNewLine(comment);
+    }
+
+    @Override
+    public void close() throws IOException {
+        out.close();
+    }
+}
\ No newline at end of file
diff -Nru htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/SequenceRegion.java htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/SequenceRegion.java
--- htsjdk-2.22.0+dfsg/src/main/java/htsjdk/tribble/gff/SequenceRegion.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/gff/SequenceRegion.java	2020-07-08 16:28:01.000000000 +0000
@@ -9,7 +9,8 @@
     private final int start;
     private final int end;
     private final String contig;
-    private boolean isCircular;
+    private Boolean isCircular;
+    private int hashCode;
 
     SequenceRegion(final String contig, final int start, final int end) {
         this(contig, start, end, false);
@@ -20,10 +21,12 @@
         this.start = start;
         this.end = end;
         this.isCircular = isCircular;
+        hashCode = computeHashCode();
     }
 
     void setCircular(final boolean isCircular) {
         this.isCircular = isCircular;
+        hashCode = computeHashCode();
     }
 
     void setCircular() {
@@ -41,9 +44,28 @@
 
     public boolean isCircular(){return  isCircular;}
 
-    public boolean equals(final SequenceRegion other) {
-        return other.start == start && other.end==end && other.contig.equals(contig) && other.isCircular == isCircular;
+    @Override
+    public boolean equals(Object other) {
+        if (other == this) {
+            return true;
+        }
+
+        if (!(other instanceof SequenceRegion)) {
+            return false;
+        }
+
+        final SequenceRegion otherSequenceRegion = (SequenceRegion) other;
+        return otherSequenceRegion.start == start && otherSequenceRegion.end==end && otherSequenceRegion.contig.equals(contig) && otherSequenceRegion.isCircular == isCircular;
     }
 
+    private int computeHashCode() {
+        int hash = contig.hashCode();
+        hash = 31 * hash + start;
+        hash = 31 * hash + end;
+        hash = 31 * hash + isCircular.hashCode();
+        return hash;
+    }
 
+    @Override
+    public int hashCode() { return hashCode;}
 }
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -3,10 +3,11 @@
 import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloserUtil;
 import org.testng.annotations.Test;
-import static org.testng.Assert.assertEquals;
 
 import java.io.File;
 
+import static org.testng.Assert.assertEquals;
+
 /**
  * Test the fix of a bug reported by s-andrews in which the use of an arithmetic rather than a logical right shift in BinaryCigarCodec.binaryCigarToCigarElement()
  * causes an overflow in the CIGAR when reading a BAM file for a read that spans a very large intron.
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -1,6 +1,7 @@
 package htsjdk.samtools.seekablestream;
 
 import htsjdk.HtsjdkTest;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.TestUtil;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
@@ -8,13 +9,16 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
 import java.net.URL;
+import java.nio.file.Paths;
 
 public class SeekableStreamFactoryTest extends HtsjdkTest {
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools");
 
     @Test
-    public void testIsFilePath() throws Exception {
+    public void testIsFilePath() {
         Assert.assertEquals(SeekableStreamFactory.isFilePath("x"), true);
         Assert.assertEquals(SeekableStreamFactory.isFilePath(""), true);
         Assert.assertEquals(SeekableStreamFactory.isFilePath("http://broadinstitute.org"), false);
@@ -23,7 +27,7 @@
     }
 
     @DataProvider(name="getStreamForData")
-    public Object[][] getStreamForData() throws Exception {
+    public Object[][] getStreamForData() throws MalformedURLException {
         return new Object[][] {
                 { new File(TEST_DATA_DIR, "BAMFileIndexTest/index_test.bam").getAbsolutePath(),
                         new File(TEST_DATA_DIR, "BAMFileIndexTest/index_test.bam").getAbsolutePath() },
@@ -43,4 +47,29 @@
         Assert.assertEquals(SeekableStreamFactory.getInstance().getStreamFor(path).getSource(), expectedPath);
     }
 
+    @Test
+    public void testPathWithEmbeddedSpace() throws IOException {
+        final File testBam =  new File(TEST_DATA_DIR, "BAMFileIndexTest/index_test.bam");
+
+        //create a temp dir with a space in the name and copy the test file there
+        final File tempDir = IOUtil.createTempDir("test spaces", "");
+        Assert.assertTrue(tempDir.getAbsolutePath().contains(" "));
+        tempDir.deleteOnExit();
+        final File inputBam = new File(tempDir, "index_test.bam");
+        inputBam.deleteOnExit();
+        IOUtil.copyFile(testBam, inputBam);
+
+        // make sure the input string we use is URL-encoded
+        final String inputString = Paths.get(inputBam.getAbsolutePath()).toUri().toString();
+        Assert.assertFalse(inputString.contains(" "));
+        Assert.assertTrue(inputString.contains("%20"));
+
+        try (final SeekableStream seekableStream =
+                     SeekableStreamFactory.getInstance().getStreamFor(inputString)) {
+            final int BYTES_TO_READ = 10;
+            Assert.assertEquals(seekableStream.read(new byte[BYTES_TO_READ], 0,BYTES_TO_READ), BYTES_TO_READ);
+        }
+
+    }
+
 }
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -25,10 +25,13 @@
 
 import htsjdk.samtools.SAMRecordSetBuilder;
 import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
+import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.util.Arrays;
@@ -311,7 +314,7 @@
         EdgeReadIterator iterator = new EdgeReadIterator(builder.getSamReader(), intervals);
         int locusPosition = 40;
         while (iterator.hasNext()) {
-            AbstractLocusInfo<EdgingRecordAndOffset> next = iterator.next();
+            final AbstractLocusInfo<EdgingRecordAndOffset> next = iterator.next();
             int position = next.getPosition();
             assertEquals(locusPosition++, position);
             if (position == 40) {
@@ -333,6 +336,24 @@
         assertEquals(81, locusPosition);
     }
 
+    @Test
+    public void testNoGapsInLocusAccumulator() {
+        final SamReader reader = SamReaderFactory.make().open(new File("src/test/resources/htsjdk/samtools/util/sliver.sam"));
+        final EdgeReadIterator iterator = new EdgeReadIterator(reader, null);
+
+        AbstractLocusInfo<EdgingRecordAndOffset> previous = null;
+        int counter = 0;
+        while (iterator.hasNext() && (previous == null || previous.getPosition() < 1_000_000)) {
+            counter++;
+            final AbstractLocusInfo<EdgingRecordAndOffset> next = iterator.next();
+            if (previous != null) {
+                Assert.assertEquals(next.getPosition(), previous.getPosition() + 1);
+            }
+            previous = next;
+        }
+        Assert.assertEquals(counter, 1_000_000);
+    }
+
     /**
      * Test for intersecting interval for read with a deletion in the middle
      */
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -23,7 +23,6 @@
  */
 package htsjdk.samtools.util;
 
-
 import htsjdk.HtsjdkTest;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
@@ -32,18 +31,16 @@
 import org.testng.annotations.Test;
 
 /**
- * 
  * @author Mariia_Zueva@epam.com, EPAM Systems, Inc. <www.epam.com>
- *
  */
 
 public class EdgingRecordAndOffsetTest extends HtsjdkTest {
-    private final byte[] qualities = {30, 50, 50, 60, 60, 70 ,70, 70, 80, 90};
+    private final byte[] qualities = {30, 50, 50, 60, 60, 70, 70, 70, 80, 90};
     private final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T', 'T', 'C'};
     private SAMRecord record;
 
     @BeforeTest
-    public void setUp(){
+    public void setUp() {
         record = new SAMRecord(new SAMFileHeader());
         record.setReadName("testRecord");
         record.setReadBases(bases);
@@ -51,7 +48,7 @@
     }
 
     @Test
-    public void testConstructor(){
+    public void testConstructor() {
         EdgingRecordAndOffset typedRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 0, 10, 3);
         Assert.assertEquals(qualities, typedRecordAndOffset.getBaseQualities());
         Assert.assertEquals(bases, typedRecordAndOffset.getRecord().getReadBases());
@@ -62,7 +59,7 @@
     }
 
     @Test
-    public void  testGetSetStart(){
+    public void testGetSetStart() {
         EdgingRecordAndOffset typedRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 0, 10, 3);
         EdgingRecordAndOffset typedRecordAndOffsetEnd = EdgingRecordAndOffset.createEndRecord(typedRecordAndOffset);
         Assert.assertEquals(typedRecordAndOffset, typedRecordAndOffsetEnd.getStart());
@@ -70,7 +67,7 @@
     }
 
     @Test
-    public void testNotEqualsTypedRecords(){
+    public void testNotEqualsTypedRecords() {
         EdgingRecordAndOffset typedRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 0, 10, 3);
         EdgingRecordAndOffset secondEdgingRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 5, 10, 3);
         Assert.assertNotEquals(typedRecordAndOffset.getBaseQuality(), secondEdgingRecordAndOffset.getBaseQuality());
@@ -78,14 +75,14 @@
     }
 
     @Test
-    public void testGetOffset(){
+    public void testGetOffset() {
         EdgingRecordAndOffset secondEdgingRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 5, 10, 3);
         Assert.assertEquals(70, secondEdgingRecordAndOffset.getBaseQuality());
         Assert.assertEquals('C', secondEdgingRecordAndOffset.getReadBase());
     }
 
     @Test
-    public void testGetQualityAtPosition(){
+    public void testGetQualityAtPosition() {
         EdgingRecordAndOffset secondEdgingRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 0, 10, 1);
         Assert.assertEquals(50, secondEdgingRecordAndOffset.getBaseQuality(2));
     }
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3CodecTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3CodecTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3CodecTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3CodecTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -4,6 +4,7 @@
 import htsjdk.HtsjdkTest;
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.TestUtils;
+import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.annotation.Strand;
 import htsjdk.tribble.readers.LineIterator;
 import org.testng.Assert;
@@ -14,6 +15,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -67,6 +69,24 @@
         Assert.assertEquals(countTotalFeatures, expectedTotalFeatures);
     }
 
+    @Test(dataProvider = "basicDecodeDataProvider")
+    public void basicShallowDecodeTest(final Path inputGff3, final int expectedTotalFeatures) throws IOException {
+        Assert.assertTrue((new Gff3Codec(Gff3Codec.DecodeDepth.SHALLOW)).canDecode(inputGff3.toAbsolutePath().toString()));
+        final AbstractFeatureReader<Gff3Feature, LineIterator> reader = AbstractFeatureReader.getFeatureReader(inputGff3.toAbsolutePath().toString(), null, new Gff3Codec(Gff3Codec.DecodeDepth.SHALLOW), false);
+        int countTotalFeatures = 0;
+        for (final Gff3Feature feature : reader.iterator()) {
+            countTotalFeatures++;
+            //shouldn't have any children, parents, or cofeatures
+            Assert.assertEquals(feature.getAncestors().size(), 0);
+            Assert.assertEquals(feature.getDescendents().size(), 0);
+            Assert.assertEquals(feature.getCoFeatures().size(), 0);
+        }
+
+        Assert.assertEquals(countTotalFeatures, expectedTotalFeatures);
+
+
+    }
+
     @DataProvider(name = "testGZippedDataProvider")
     Object[][] testGZippedDataProvider(){
         return new Object[][] {
@@ -86,7 +106,6 @@
         final AbstractFeatureReader<Gff3Feature, LineIterator> reader = AbstractFeatureReader.getFeatureReader(inputGff3.toAbsolutePath().toString(), null, new Gff3Codec(), false);
         final AbstractFeatureReader<Gff3Feature, LineIterator> readerGZipped = AbstractFeatureReader.getFeatureReader(inputGff3GZipped.toAbsolutePath().toString(), null, new Gff3Codec(), false);
 
-
         final Set<Gff3Feature> topLevelFeatures = new HashSet<>();
         final Set<Gff3Feature> topLevelFeaturesGZipped = new HashSet<>();
 
@@ -101,6 +120,34 @@
         Assert.assertEquals(topLevelFeatures, topLevelFeaturesGZipped);
     }
 
+    @Test(dataProvider = "testGZippedDataProvider")
+    public void testGZippedShallow(final Path inputGff3, final Path inputGff3GZipped) throws IOException {
+        Assert.assertTrue((new Gff3Codec()).canDecode(inputGff3.toAbsolutePath().toString()));
+        Assert.assertTrue((new Gff3Codec()).canDecode(inputGff3GZipped.toAbsolutePath().toString()));
+
+        final AbstractFeatureReader<Gff3Feature, LineIterator> reader = AbstractFeatureReader.getFeatureReader(inputGff3.toAbsolutePath().toString(), null, new Gff3Codec(Gff3Codec.DecodeDepth.SHALLOW), false);
+        final AbstractFeatureReader<Gff3Feature, LineIterator> readerGZipped = AbstractFeatureReader.getFeatureReader(inputGff3GZipped.toAbsolutePath().toString(), null, new Gff3Codec(Gff3Codec.DecodeDepth.SHALLOW), false);
+
+        final Set<Gff3Feature> features = new HashSet<>();
+        final Set<Gff3Feature> featuresGZipped = new HashSet<>();
+
+        for (final Gff3Feature feature : reader.iterator()) {
+            features.add(feature);
+            Assert.assertEquals(feature.getAncestors().size(), 0);
+            Assert.assertEquals(feature.getDescendents().size(), 0);
+            Assert.assertEquals(feature.getCoFeatures().size(), 0);
+        }
+
+        for (final Gff3Feature feature : readerGZipped.iterator()) {
+            featuresGZipped.add(feature);
+            Assert.assertEquals(feature.getAncestors().size(), 0);
+            Assert.assertEquals(feature.getDescendents().size(), 0);
+            Assert.assertEquals(feature.getCoFeatures().size(), 0);
+        }
+
+        Assert.assertEquals(features, featuresGZipped);
+    }
+
     @DataProvider(name = "sequenceRegionValidationDataProvider")
     Object[][] sequenceRegionValidationDataProvider() {
         return new Object[][] {
@@ -132,7 +179,7 @@
         Assert.assertEquals(feature.getSource(), "a source & also a str*)%nge source");
         Assert.assertEquals(feature.getType(), "a region");
         Assert.assertEquals(feature.getID(), "this is the ID of this wacky feature^&%##$%*&>,. ,.");
-        Assert.assertEquals(feature.getAttribute("Another key"), "Another=value");
+        Assert.assertEquals(feature.getAttribute("Another key"), Arrays.asList("Another=value", "And a second, value"));
     }
 
 
@@ -151,113 +198,113 @@
 
         final Set<Gff3Feature> canonicalGeneFeatures = new HashSet<>();
 
-        final Gff3FeatureImpl canonicalGene_gene00001 = new Gff3FeatureImpl("ctg123", ".", "gene", 1000, 9000, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene00001", "Name", "EDEN"));
+        final Gff3FeatureImpl canonicalGene_gene00001 = new Gff3FeatureImpl("ctg123", ".", "gene", 1000, 9000, 1030d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene00001"), "Name", Collections.singletonList("EDEN")));
         canonicalGeneFeatures.add(canonicalGene_gene00001);
 
-        final Gff3FeatureImpl canonicalGene_tfbs00001 = new Gff3FeatureImpl("ctg123", ".", "TF_binding_site", 1000, 1012, Strand.POSITIVE, -1, ImmutableMap.of("ID", "tfbs00001", "Parent", "gene00001"));
+        final Gff3FeatureImpl canonicalGene_tfbs00001 = new Gff3FeatureImpl("ctg123", ".", "TF_binding_site", 1000, 1012, 0.999d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("tfbs00001"), "Parent", Collections.singletonList("gene00001")));
         canonicalGene_tfbs00001.addParent(canonicalGene_gene00001);
         canonicalGeneFeatures.add(canonicalGene_tfbs00001);
 
-        final Gff3FeatureImpl canonicalGene_mRNA00001 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1050, 9000, Strand.POSITIVE, -1, ImmutableMap.of("ID", "mRNA00001", "Name", "EDEN.1", "Parent", "gene00001"));
+        final Gff3FeatureImpl canonicalGene_mRNA00001 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1050, 9000, 1.37d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("mRNA00001"), "Name", Collections.singletonList("EDEN.1"), "Parent", Collections.singletonList("gene00001")));
         canonicalGene_mRNA00001.addParent(canonicalGene_gene00001);
         canonicalGeneFeatures.add(canonicalGene_mRNA00001);
 
-        final Gff3FeatureImpl canonicalGene_mRNA00002 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1050, 9000, Strand.POSITIVE, -1, ImmutableMap.of("ID", "mRNA00002", "Name", "EDEN.2", "Parent", "gene00001"));
+        final Gff3FeatureImpl canonicalGene_mRNA00002 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1050, 9000, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("mRNA00002"), "Name", Collections.singletonList("EDEN.2"), "Parent", Collections.singletonList("gene00001")));
         canonicalGene_mRNA00002.addParent(canonicalGene_gene00001);
         canonicalGeneFeatures.add(canonicalGene_mRNA00002);
 
-        final Gff3FeatureImpl canonicalGene_mRNA00003 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1300, 9000, Strand.POSITIVE, -1, ImmutableMap.of("ID", "mRNA00003", "Name", "EDEN.3", "Parent", "gene00001"));
+        final Gff3FeatureImpl canonicalGene_mRNA00003 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1300, 9000, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("EDEN.3"), "Parent", Collections.singletonList("gene00001")));
         canonicalGene_mRNA00003.addParent(canonicalGene_gene00001);
         canonicalGeneFeatures.add(canonicalGene_mRNA00003);
 
-        final Gff3FeatureImpl canonicalGene_exon00001 = new Gff3FeatureImpl("ctg123", ".", "exon", 1300, 1500, Strand.POSITIVE, -1, ImmutableMap.of("ID", "exon00001", "Parent", "mRNA00003"));
+        final Gff3FeatureImpl canonicalGene_exon00001 = new Gff3FeatureImpl("ctg123", ".", "exon", 1300, 1500, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("exon00001"), "Parent", Collections.singletonList("mRNA00003")));
         canonicalGene_exon00001.addParent(canonicalGene_mRNA00003);
         canonicalGeneFeatures.add(canonicalGene_exon00001);
 
-        final Gff3FeatureImpl canonicalGene_exon00002 = new Gff3FeatureImpl("ctg123", ".", "exon", 1050, 1500, Strand.POSITIVE, -1, ImmutableMap.of("ID", "exon00002", "Parent", "mRNA00001,mRNA00002"));
+        final Gff3FeatureImpl canonicalGene_exon00002 = new Gff3FeatureImpl("ctg123", ".", "exon", 1050, 1500, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("exon00002"), "Parent", Arrays.asList("mRNA00001", "mRNA00002")));
         canonicalGene_exon00002.addParent(canonicalGene_mRNA00001);
         canonicalGene_exon00002.addParent(canonicalGene_mRNA00002);
         canonicalGeneFeatures.add(canonicalGene_exon00002);
 
-        final Gff3FeatureImpl canonicalGene_exon00003 = new Gff3FeatureImpl("ctg123", ".", "exon", 3000, 3902, Strand.POSITIVE, -1, ImmutableMap.of("ID", "exon00003", "Parent", "mRNA00001,mRNA00003"));
+        final Gff3FeatureImpl canonicalGene_exon00003 = new Gff3FeatureImpl("ctg123", ".", "exon", 3000, 3902, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("exon00003"), "Parent", Arrays.asList("mRNA00001", "mRNA00003")));
         canonicalGene_exon00003.addParent(canonicalGene_mRNA00001);
         canonicalGene_exon00003.addParent(canonicalGene_mRNA00003);
         canonicalGeneFeatures.add(canonicalGene_exon00003);
 
-        final Gff3FeatureImpl canonicalGene_exon00004 = new Gff3FeatureImpl("ctg123", ".", "exon", 5000, 5500, Strand.POSITIVE, -1, ImmutableMap.of("ID", "exon00004", "Parent", "mRNA00001,mRNA00002,mRNA00003"));
+        final Gff3FeatureImpl canonicalGene_exon00004 = new Gff3FeatureImpl("ctg123", ".", "exon", 5000, 5500, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("exon00004"), "Parent", Arrays.asList("mRNA00001", "mRNA00002", "mRNA00003")));
         canonicalGene_exon00004.addParent(canonicalGene_mRNA00001);
         canonicalGene_exon00004.addParent(canonicalGene_mRNA00002);
         canonicalGene_exon00004.addParent(canonicalGene_mRNA00003);
         canonicalGeneFeatures.add(canonicalGene_exon00004);
 
-        final Gff3FeatureImpl canonicalGene_exon00005 = new Gff3FeatureImpl("ctg123", ".", "exon", 7000, 9000, Strand.POSITIVE, -1, ImmutableMap.of("ID", "exon00005", "Parent", "mRNA00001,mRNA00002,mRNA00003"));
+        final Gff3FeatureImpl canonicalGene_exon00005 = new Gff3FeatureImpl("ctg123", ".", "exon", 7000, 9000, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("exon00005"), "Parent", Arrays.asList("mRNA00001", "mRNA00002", "mRNA00003")));
         canonicalGene_exon00005.addParent(canonicalGene_mRNA00001);
         canonicalGene_exon00005.addParent(canonicalGene_mRNA00002);
         canonicalGene_exon00005.addParent(canonicalGene_mRNA00003);
         canonicalGeneFeatures.add(canonicalGene_exon00005);
 
-        final Gff3FeatureImpl canonicalGene_cds00001_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 1201, 1500, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00001", "Parent", "mRNA00001", "Name", "edenprotein.1"));
+        final Gff3FeatureImpl canonicalGene_cds00001_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 1201, 1500, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00001"), "Parent", Collections.singletonList("mRNA00001"), "Name", Collections.singletonList("edenprotein.1")));
         canonicalGene_cds00001_1.addParent(canonicalGene_mRNA00001);
         canonicalGeneFeatures.add(canonicalGene_cds00001_1);
 
-        final Gff3FeatureImpl canonicalGene_cds00001_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 3000, 3902, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00001", "Parent", "mRNA00001", "Name", "edenprotein.1"));
+        final Gff3FeatureImpl canonicalGene_cds00001_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 3000, 3902, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00001"), "Parent", Collections.singletonList("mRNA00001"), "Name", Collections.singletonList("edenprotein.1")));
         canonicalGene_cds00001_2.addParent(canonicalGene_mRNA00001);
         canonicalGene_cds00001_2.addCoFeature(canonicalGene_cds00001_1);
         canonicalGeneFeatures.add(canonicalGene_cds00001_2);
 
-        final Gff3FeatureImpl canonicalGene_cds00001_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00001", "Parent", "mRNA00001", "Name", "edenprotein.1"));
+        final Gff3FeatureImpl canonicalGene_cds00001_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00001"), "Parent", Collections.singletonList("mRNA00001"), "Name", Collections.singletonList("edenprotein.1")));
         canonicalGene_cds00001_3.addParent(canonicalGene_mRNA00001);
         canonicalGene_cds00001_3.addCoFeature(canonicalGene_cds00001_1);
         canonicalGene_cds00001_3.addCoFeature(canonicalGene_cds00001_2);
         canonicalGeneFeatures.add(canonicalGene_cds00001_3);
 
-        final Gff3FeatureImpl canonicalGene_cds00001_4 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00001", "Parent", "mRNA00001", "Name", "edenprotein.1"));
+        final Gff3FeatureImpl canonicalGene_cds00001_4 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00001"), "Parent", Collections.singletonList("mRNA00001"), "Name", Collections.singletonList("edenprotein.1")));
         canonicalGene_cds00001_4.addParent(canonicalGene_mRNA00001);
         canonicalGene_cds00001_4.addCoFeature(canonicalGene_cds00001_1);
         canonicalGene_cds00001_4.addCoFeature(canonicalGene_cds00001_2);
         canonicalGene_cds00001_4.addCoFeature(canonicalGene_cds00001_3);
         canonicalGeneFeatures.add(canonicalGene_cds00001_4);
 
-        final Gff3FeatureImpl canonicalGene_cds00002_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 1201, 1500, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00002", "Parent", "mRNA00002", "Name", "edenprotein.2"));
+        final Gff3FeatureImpl canonicalGene_cds00002_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 1201, 1500, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00002"), "Parent", Collections.singletonList("mRNA00002"), "Name", Collections.singletonList("edenprotein.2")));
         canonicalGene_cds00002_1.addParent(canonicalGene_mRNA00002);
         canonicalGeneFeatures.add(canonicalGene_cds00002_1);
 
-        final Gff3FeatureImpl canonicalGene_cds00002_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00002", "Parent", "mRNA00002", "Name", "edenprotein.2"));
+        final Gff3FeatureImpl canonicalGene_cds00002_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00002"), "Parent", Collections.singletonList("mRNA00002"), "Name", Collections.singletonList("edenprotein.2")));
         canonicalGene_cds00002_2.addParent(canonicalGene_mRNA00002);
         canonicalGene_cds00002_2.addCoFeature(canonicalGene_cds00002_1);
         canonicalGeneFeatures.add(canonicalGene_cds00002_2);
 
-        final Gff3FeatureImpl canonicalGene_cds00002_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00002", "Parent", "mRNA00002", "Name", "edenprotein.2"));
+        final Gff3FeatureImpl canonicalGene_cds00002_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00002"), "Parent", Collections.singletonList("mRNA00002"), "Name", Collections.singletonList("edenprotein.2")));
         canonicalGene_cds00002_3.addParent(canonicalGene_mRNA00002);
         canonicalGene_cds00002_3.addCoFeature(canonicalGene_cds00002_1);
         canonicalGene_cds00002_3.addCoFeature(canonicalGene_cds00002_2);
         canonicalGeneFeatures.add(canonicalGene_cds00002_3);
 
-        final Gff3FeatureImpl canonicalGene_cds00003_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 3301, 3902, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00003", "Parent", "mRNA00003", "Name", "edenprotein.3"));
+        final Gff3FeatureImpl canonicalGene_cds00003_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 3301, 3902, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00003"), "Parent", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("edenprotein.3")));
         canonicalGene_cds00003_1.addParent(canonicalGene_mRNA00003);
         canonicalGeneFeatures.add(canonicalGene_cds00003_1);
 
-        final Gff3FeatureImpl canonicalGene_cds00003_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, Strand.POSITIVE, 1, ImmutableMap.of("ID", "cds00003", "Parent", "mRNA00003", "Name", "edenprotein.3"));
+        final Gff3FeatureImpl canonicalGene_cds00003_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, -1d, Strand.POSITIVE, 1, ImmutableMap.of("ID", Collections.singletonList("cds00003"), "Parent", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("edenprotein.3")));
         canonicalGene_cds00003_2.addParent(canonicalGene_mRNA00003);
         canonicalGene_cds00003_2.addCoFeature(canonicalGene_cds00003_1);
         canonicalGeneFeatures.add(canonicalGene_cds00003_2);
 
-        final Gff3FeatureImpl canonicalGene_cds00003_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, Strand.POSITIVE, 1, ImmutableMap.of("ID", "cds00003", "Parent", "mRNA00003", "Name", "edenprotein.3"));
+        final Gff3FeatureImpl canonicalGene_cds00003_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, -1d, Strand.POSITIVE, 1, ImmutableMap.of("ID", Collections.singletonList("cds00003"), "Parent", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("edenprotein.3")));
         canonicalGene_cds00003_3.addParent(canonicalGene_mRNA00003);
         canonicalGene_cds00003_3.addCoFeature(canonicalGene_cds00003_1);
         canonicalGene_cds00003_3.addCoFeature(canonicalGene_cds00003_2);
         canonicalGeneFeatures.add(canonicalGene_cds00003_3);
 
-        final Gff3FeatureImpl canonicalGene_cds00004_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 3391, 3902, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds00004", "Parent", "mRNA00003", "Name", "edenprotein.4"));
+        final Gff3FeatureImpl canonicalGene_cds00004_1 = new Gff3FeatureImpl("ctg123", ".", "CDS", 3391, 3902, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds00004"), "Parent", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("edenprotein.4")));
         canonicalGene_cds00004_1.addParent(canonicalGene_mRNA00003);
         canonicalGeneFeatures.add(canonicalGene_cds00004_1);
         
-        final Gff3FeatureImpl canonicalGene_cds00004_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, Strand.POSITIVE, 1, ImmutableMap.of("ID", "cds00004", "Parent", "mRNA00003", "Name", "edenprotein.4"));
+        final Gff3FeatureImpl canonicalGene_cds00004_2 = new Gff3FeatureImpl("ctg123", ".", "CDS", 5000, 5500, -1d, Strand.POSITIVE, 1, ImmutableMap.of("ID", Collections.singletonList("cds00004"), "Parent", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("edenprotein.4")));
         canonicalGene_cds00004_2.addParent(canonicalGene_mRNA00003);
         canonicalGene_cds00004_2.addCoFeature(canonicalGene_cds00004_1);
         canonicalGeneFeatures.add(canonicalGene_cds00004_2);
 
-        final Gff3FeatureImpl canonicalGene_cds00004_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, Strand.POSITIVE, 1, ImmutableMap.of("ID", "cds00004", "Parent", "mRNA00003", "Name", "edenprotein.4"));
+        final Gff3FeatureImpl canonicalGene_cds00004_3 = new Gff3FeatureImpl("ctg123", ".", "CDS", 7000, 7600, -1d, Strand.POSITIVE, 1, ImmutableMap.of("ID", Collections.singletonList("cds00004"), "Parent", Collections.singletonList("mRNA00003"), "Name", Collections.singletonList("edenprotein.4")));
         canonicalGene_cds00004_3.addParent(canonicalGene_mRNA00003);
         canonicalGene_cds00004_3.addCoFeature(canonicalGene_cds00004_1);
         canonicalGene_cds00004_3.addCoFeature(canonicalGene_cds00004_2);
@@ -271,40 +318,40 @@
 
         final Set<Gff3Feature> polycisctronicTranscriptFeatures = new HashSet<>();
 
-        final Gff3FeatureImpl polycistronicTranscript_gene01 = new Gff3FeatureImpl("chrX", ".", "gene", 100, 200, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene01", "name", "resA"));
-        final Gff3FeatureImpl polycistronicTranscript_gene02 = new Gff3FeatureImpl("chrX", ".", "gene", 250, 350, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene02", "name", "resB"));
-        final Gff3FeatureImpl polycistronicTranscript_gene03 = new Gff3FeatureImpl("chrX", ".", "gene", 400, 500, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene03", "name", "resX"));
-        final Gff3FeatureImpl polycistronicTranscript_gene04 = new Gff3FeatureImpl("chrX", ".", "gene", 550, 650, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene04", "name", "resZ"));
+        final Gff3FeatureImpl polycistronicTranscript_gene01 = new Gff3FeatureImpl("chrX", ".", "gene", 100, 200, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "name", Collections.singletonList("resA")));
+        final Gff3FeatureImpl polycistronicTranscript_gene02 = new Gff3FeatureImpl("chrX", ".", "gene", 250, 350, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene02"), "name", Collections.singletonList("resB")));
+        final Gff3FeatureImpl polycistronicTranscript_gene03 = new Gff3FeatureImpl("chrX", ".", "gene", 400, 500, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene03"), "name", Collections.singletonList("resX")));
+        final Gff3FeatureImpl polycistronicTranscript_gene04 = new Gff3FeatureImpl("chrX", ".", "gene", 550, 650, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene04"), "name", Collections.singletonList("resZ")));
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_gene01);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_gene02);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_gene03);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_gene04);
 
-        final Gff3FeatureImpl polycistronicTranscript_mRNA = new Gff3FeatureImpl("chrX", ".", "mRNA", 100, 650, Strand.POSITIVE, -1, ImmutableMap.of("ID", "tran01", "Parent", "gene01,gene02,gene03,gene04"));
+        final Gff3FeatureImpl polycistronicTranscript_mRNA = new Gff3FeatureImpl("chrX", ".", "mRNA", 100, 650, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("tran01"), "Parent", Arrays.asList("gene01", "gene02", "gene03", "gene04")));
         polycistronicTranscript_mRNA.addParent(polycistronicTranscript_gene01);
         polycistronicTranscript_mRNA.addParent(polycistronicTranscript_gene02);
         polycistronicTranscript_mRNA.addParent(polycistronicTranscript_gene03);
         polycistronicTranscript_mRNA.addParent(polycistronicTranscript_gene04);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_mRNA);
 
-        final Gff3FeatureImpl polycistronicTranscript_exon = new Gff3FeatureImpl("chrX", ".", "exon", 100, 650, Strand.POSITIVE, -1, ImmutableMap.of("Parent", "tran01"));
+        final Gff3FeatureImpl polycistronicTranscript_exon = new Gff3FeatureImpl("chrX", ".", "exon", 100, 650, -1d, Strand.POSITIVE, -1, ImmutableMap.of("Parent", Collections.singletonList("tran01")));
         polycistronicTranscript_exon.addParent(polycistronicTranscript_mRNA);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_exon);
 
 
-        final Gff3FeatureImpl polycistronicTranscript_CDS1 = new Gff3FeatureImpl("chrX", ".", "CDS", 100, 200, Strand.POSITIVE, 0, ImmutableMap.of("Parent", "tran01", "Derives_from", "gene01"));
+        final Gff3FeatureImpl polycistronicTranscript_CDS1 = new Gff3FeatureImpl("chrX", ".", "CDS", 100, 200, -1d, Strand.POSITIVE, 0, ImmutableMap.of("Parent", Collections.singletonList("tran01"), "Derives_from", Collections.singletonList("gene01")));
         polycistronicTranscript_CDS1.addParent(polycistronicTranscript_mRNA);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_CDS1);
 
-        final Gff3FeatureImpl polycistronicTranscript_CDS2 = new Gff3FeatureImpl("chrX", ".", "CDS", 250, 350, Strand.POSITIVE, 0, ImmutableMap.of("Parent", "tran01", "Derives_from", "gene02"));
+        final Gff3FeatureImpl polycistronicTranscript_CDS2 = new Gff3FeatureImpl("chrX", ".", "CDS", 250, 350, -1d, Strand.POSITIVE, 0, ImmutableMap.of("Parent", Collections.singletonList("tran01"), "Derives_from", Collections.singletonList("gene02")));
         polycistronicTranscript_CDS2.addParent(polycistronicTranscript_mRNA);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_CDS2);
 
-        final Gff3FeatureImpl polycistronicTranscript_CDS3 = new Gff3FeatureImpl("chrX", ".", "CDS", 400, 500, Strand.POSITIVE, 0, ImmutableMap.of("Parent", "tran01", "Derives_from", "gene03"));
+        final Gff3FeatureImpl polycistronicTranscript_CDS3 = new Gff3FeatureImpl("chrX", ".", "CDS", 400, 500, -1d, Strand.POSITIVE, 0, ImmutableMap.of("Parent", Collections.singletonList("tran01"), "Derives_from", Collections.singletonList("gene03")));
         polycistronicTranscript_CDS3.addParent(polycistronicTranscript_mRNA);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_CDS3);
 
-        final Gff3FeatureImpl polycistronicTranscript_CDS4 = new Gff3FeatureImpl("chrX", ".", "CDS", 550, 650, Strand.POSITIVE, 0, ImmutableMap.of("Parent", "tran01", "Derives_from", "gene04"));
+        final Gff3FeatureImpl polycistronicTranscript_CDS4 = new Gff3FeatureImpl("chrX", ".", "CDS", 550, 650, -1d, Strand.POSITIVE, 0, ImmutableMap.of("Parent", Collections.singletonList("tran01"), "Derives_from", Collections.singletonList("gene04")));
         polycistronicTranscript_CDS4.addParent(polycistronicTranscript_mRNA);
         polycisctronicTranscriptFeatures.add(polycistronicTranscript_CDS4);
 
@@ -316,23 +363,23 @@
 
         final Set<Gff3Feature> programmedFrameshiftFeatures = new HashSet<>();
 
-        final Gff3FeatureImpl programmedFrameshift_gene = new Gff3FeatureImpl("chrX", ".", "gene", 100, 200, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene01", "name", "my_gene"));
+        final Gff3FeatureImpl programmedFrameshift_gene = new Gff3FeatureImpl("chrX", ".", "gene", 100, 200, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "name", Collections.singletonList("my_gene")));
         programmedFrameshiftFeatures.add(programmedFrameshift_gene);
 
-        final Gff3FeatureImpl programmedFrameshift_mRNA = new Gff3FeatureImpl("chrX", ".", "mRNA", 100, 200, Strand.POSITIVE, -1, ImmutableMap.of("ID", "tran01", "Parent", "gene01", "Ontology_term", "SO:1000069"));
+        final Gff3FeatureImpl programmedFrameshift_mRNA = new Gff3FeatureImpl("chrX", ".", "mRNA", 100, 200, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("tran01"), "Parent", Collections.singletonList("gene01"), "Ontology_term", Collections.singletonList("SO:1000069")));
         programmedFrameshift_mRNA.addParent(programmedFrameshift_gene);
         programmedFrameshiftFeatures.add(programmedFrameshift_mRNA);
 
-        final Gff3FeatureImpl programmedFrameshift_exon = new Gff3FeatureImpl("chrX", ".", "exon", 100, 200, Strand.POSITIVE, -1, ImmutableMap.of("ID", "exon01", "Parent", "tran01"));
+        final Gff3FeatureImpl programmedFrameshift_exon = new Gff3FeatureImpl("chrX", ".", "exon", 100, 200, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("exon01"), "Parent", Collections.singletonList("tran01")));
         programmedFrameshift_exon.addParent(programmedFrameshift_mRNA);
         programmedFrameshiftFeatures.add(programmedFrameshift_exon);
 
 
-        final Gff3FeatureImpl programmedFrameshift_CDS1_1 = new Gff3FeatureImpl("chrX", ".", "CDS", 100, 150, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds01", "Parent", "tran01"));
+        final Gff3FeatureImpl programmedFrameshift_CDS1_1 = new Gff3FeatureImpl("chrX", ".", "CDS", 100, 150, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"), "Parent",Collections.singletonList( "tran01")));
         programmedFrameshift_CDS1_1.addParent(programmedFrameshift_mRNA);
         programmedFrameshiftFeatures.add(programmedFrameshift_CDS1_1);
 
-        final Gff3FeatureImpl programmedFrameshift_CDS1_2 = new Gff3FeatureImpl("chrX", ".", "CDS", 149, 200, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds01", "Parent", "tran01"));
+        final Gff3FeatureImpl programmedFrameshift_CDS1_2 = new Gff3FeatureImpl("chrX", ".", "CDS", 149, 200, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"), "Parent", Collections.singletonList("tran01")));
         programmedFrameshift_CDS1_2.addParent(programmedFrameshift_mRNA);
         programmedFrameshift_CDS1_2.addCoFeature(programmedFrameshift_CDS1_1);
         programmedFrameshiftFeatures.add(programmedFrameshift_CDS1_2);
@@ -345,17 +392,17 @@
 
         final Set<Gff3Feature> multipleGenesFeatures = new HashSet<>();
 
-        final Gff3FeatureImpl multipleGenes_gene1 = new Gff3FeatureImpl("ctg123", ".", "gene", 1000, 1500, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene00001"));
+        final Gff3FeatureImpl multipleGenes_gene1 = new Gff3FeatureImpl("ctg123", ".", "gene", 1000, 1500, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene00001")));
         multipleGenesFeatures.add(multipleGenes_gene1);
 
-        final Gff3FeatureImpl multipleGenes_mRNA1 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1050, 1400, Strand.POSITIVE, -1, ImmutableMap.of("Parent", "gene00001"));
+        final Gff3FeatureImpl multipleGenes_mRNA1 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 1050, 1400, -1d, Strand.POSITIVE, -1, ImmutableMap.of("Parent", Collections.singletonList("gene00001")));
         multipleGenes_mRNA1.addParent(multipleGenes_gene1);
         multipleGenesFeatures.add(multipleGenes_mRNA1);
 
-        final Gff3FeatureImpl multipleGenes_gene2 = new Gff3FeatureImpl("ctg123", ".", "gene", 2000, 2500, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene00002"));
+        final Gff3FeatureImpl multipleGenes_gene2 = new Gff3FeatureImpl("ctg123", ".", "gene", 2000, 2500, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene00002")));
         multipleGenesFeatures.add(multipleGenes_gene2);
 
-        final Gff3FeatureImpl multipleGenes_mRNA2 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 2050, 2400, Strand.POSITIVE, -1, ImmutableMap.of("Parent", "gene00002"));
+        final Gff3FeatureImpl multipleGenes_mRNA2 = new Gff3FeatureImpl("ctg123", ".", "mRNA", 2050, 2400, -1d, Strand.POSITIVE, -1, ImmutableMap.of("Parent", Collections.singletonList("gene00002")));
         multipleGenes_mRNA2.addParent(multipleGenes_gene2);
         multipleGenesFeatures.add(multipleGenes_mRNA2);
 
@@ -368,7 +415,6 @@
     @Test(dataProvider = "examplesDataProvider")
     public void examplesTest(final String inputGff, final Set<Gff3Feature> expectedFeatures) throws IOException {
         final AbstractFeatureReader<Gff3Feature, LineIterator> reader = AbstractFeatureReader.getFeatureReader(inputGff, null, new Gff3Codec(), false);
-        int observedTopLevelFeatures = 0;
         int observedFeatures = 0;
         for (final Gff3Feature feature : reader.iterator()) {
 
@@ -378,4 +424,98 @@
 
         Assert.assertEquals(observedFeatures, expectedFeatures.size());
     }
+
+    @DataProvider(name = "directiveDataProvider")
+    public Object[][] directiveDataProvider() {
+        return new Object[][] {
+                {"##gff-version 3.1.25", Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE, "3.1.25"},
+                {"##gff-version 3.7", Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE, "3.7"},
+                {"##gff-version 3", Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE, "3"},
+                {"##gff-version 3.112.25.4.2", Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE, "3.112.25.4.2"},
+                {"##gff-version 2.7", null, null},
+                {"##sequence-region chr10 250 277", Gff3Codec.Gff3Directive.SEQUENCE_REGION_DIRECTIVE, new SequenceRegion("chr10", 250, 277)},
+                {"###", Gff3Codec.Gff3Directive.FLUSH_DIRECTIVE, null},
+                {"####", null, null},
+                {"##FASTA", Gff3Codec.Gff3Directive.FASTA_DIRECTIVE, null}
+        };
+    }
+
+    @Test(dataProvider = "directiveDataProvider")
+    public void directiveTest(final String line, final Gff3Codec.Gff3Directive expectedDirectiveType, final Object expectedDecodedDirective) throws IOException {
+        final Gff3Codec.Gff3Directive directive = Gff3Codec.Gff3Directive.toDirective(line);
+        Assert.assertEquals(directive, expectedDirectiveType);
+        if (directive != null) {
+            Assert.assertEquals(directive.decode(line), expectedDecodedDirective);
+            if (expectedDecodedDirective != null) {
+                Assert.assertEquals(directive.encode(expectedDecodedDirective), line);
+            }
+        }
+    }
+
+    @DataProvider(name = "directiveEncodingDataProvider")
+    public Object [][] directiveEncodingDataProvider() {
+        return new Object[][] {
+                {Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE, "3.1.3", "##gff-version 3.1.3"},
+                {Gff3Codec.Gff3Directive.SEQUENCE_REGION_DIRECTIVE, new SequenceRegion("theContig", 101, 170), "##sequence-region theContig 101 170"},
+                {Gff3Codec.Gff3Directive.FLUSH_DIRECTIVE, null, "###"},
+                {Gff3Codec.Gff3Directive.FASTA_DIRECTIVE, null, "##FASTA"}
+        };
+    }
+
+    @Test(dataProvider = "directiveEncodingDataProvider")
+    public void directiveEncodingTest(final Gff3Codec.Gff3Directive directive, final Object object, final String expectedEncoding) {
+        final String encoding = directive.encode(object);
+
+        Assert.assertEquals(encoding, expectedEncoding);
+    }
+
+    @DataProvider(name = "version3InvalidDirectives")
+    public Object[][] version3InvalidDirectivesDataProvider() {
+        return new Object[][] {
+                {"3.1.a"},
+                {"2"},
+                {"2.1"},
+                {".3.1"}
+        };
+    }
+
+    @Test(dataProvider = "version3InvalidDirectives", expectedExceptions = TribbleException.class)
+    public void version3InvalidDirectivesTest(final String v3Directive) {
+        Gff3Codec.Gff3Directive.VERSION3_DIRECTIVE.encode(v3Directive);
+    }
+
+    @DataProvider(name = "decodeAttributeValueDataProvider")
+    public Object[][] decodeAttributeValueDataProvider() {
+        return new Object[][] {
+                {"value1, value2, value3", Arrays.asList("value1", "value2", "value3")},
+                {"value1, value %3B with %3D special %26 encoded %2C characters, value3", Arrays.asList("value1", "value ; with = special & encoded , characters", "value3")}
+        };
+    }
+
+    @Test(dataProvider = "decodeAttributeValueDataProvider")
+    public void decodeAttributeValueTest(final String attributeValueString, final List<String> expectedAttributeValues) {
+        final List<String> attributeValues = Gff3Codec.decodeAttributeValue(attributeValueString);
+
+        Assert.assertEquals(attributeValues, expectedAttributeValues);
+    }
+
+    @DataProvider(name = "extractSingleAttributeDataProvider")
+    public Object[][] extractSingleAttributeDataProvider() {
+        return new Object[][] {
+                {null, null, false}, //null returns null
+                {Collections.emptyList(), null, false}, //empty returns null
+                {Collections.singletonList("single value"), "single value", false}, //single value returns single value
+                {Arrays.asList("value1", "value2"), null, true} //multiple values throws exception
+        };
+    }
+
+    @Test(dataProvider = "extractSingleAttributeDataProvider")
+    public void extractSingleAttributeTest(final List<String> attributes, final String expectedSingleAttribute, final boolean expectException) {
+        if (expectException) {
+            Assert.assertThrows(() -> Gff3Codec.extractSingleAttribute(attributes));
+        } else {
+            final String singleAttribute = Gff3Codec.extractSingleAttribute(attributes);
+            Assert.assertEquals(singleAttribute, expectedSingleAttribute);
+        }
+    }
 }
\ No newline at end of file
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3FeatureTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3FeatureTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3FeatureTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3FeatureTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -23,42 +23,42 @@
     @DataProvider(name = "equalityTestDataProvider")
     public Object[][] equalityTestDatProvider() {
         final ArrayList<Object[]> examples = new ArrayList<>();
-        examples.add(new Object[] {new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01")),
-                new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01")), true});
-        examples.add(new Object[] {new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01")),
-                new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01")), true});
+        examples.add(new Object[] {new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"))),
+                new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"))), true});
+        examples.add(new Object[] {new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01"))),
+                new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01"))), true});
 
         //two features with same baseData, one with child (or parent) feature, one without
-        final Gff3FeatureImpl feature1_1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature2_1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature3_1 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature1_1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature2_1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature3_1 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature3_1.addParent(feature1_1);
-        final Gff3FeatureImpl feature4_1 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature4_1 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
 
         examples.add(new Object[] {feature1_1, feature2_1, false});
         examples.add(new Object[] {feature3_1, feature4_1, false});
 
         //give both genes child feature
-        final Gff3FeatureImpl feature1_2 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature2_2 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature3_2 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, -0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature1_2 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature2_2 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature3_2 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, -0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature3_2.addParent(feature1_2);
-        final Gff3FeatureImpl feature4_2 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature4_2 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature4_2.addParent(feature2_2);
 
         examples.add(new Object[] {feature1_2, feature2_2, true});
         examples.add(new Object[] {feature3_2, feature4_2, true});
 
         //give one cds a co-feature
-        final Gff3FeatureImpl feature1_3 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature2_3 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature3_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature1_3 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature2_3 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature3_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature3_3.addParent(feature1_3);
-        final Gff3FeatureImpl feature4_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature4_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature4_3.addParent(feature2_3);
-        final Gff3FeatureImpl feature5_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature5_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature5_3.addParent(feature1_3);
-        final Gff3FeatureImpl feature6_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature6_3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
 
         feature3_3.addCoFeature(feature5_3);
 
@@ -67,15 +67,15 @@
         examples.add(new Object[] {feature5_3, feature6_3, false});
 
         //give both cds co-features
-        final Gff3FeatureImpl feature1_4 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature2_4 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature3_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature1_4 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature2_4 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature3_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature3_4.addParent(feature1_4);
-        final Gff3FeatureImpl feature4_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature4_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature4_4.addParent(feature2_4);
-        final Gff3FeatureImpl feature5_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature5_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature5_4.addParent(feature1_4);
-        final Gff3FeatureImpl feature6_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature6_4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1080, 1150, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature6_4.addParent(feature2_4);
 
         feature3_4.addCoFeature(feature5_4);
@@ -99,8 +99,8 @@
     @Test
     public void testChildren() {
         //test that when a feature has a parent it is added as it's parent's child
-        final Gff3FeatureImpl feature1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature2 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature2 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature2.addParent(feature1);
 
         Assert.assertTrue(feature1.getChildren().contains(feature2));
@@ -110,12 +110,12 @@
     @Test
     public void testCofeatures() {
         //test that when a adding a cofeature it is reciprocated
-        final Gff3FeatureImpl region = new Gff3FeatureImpl("chr1", ".", "region", 1, 10000, Strand.NONE, -1, ImmutableMap.of("ID", "region01"));
-        final Gff3FeatureImpl feature1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01", "Parent", "region01"));
+        final Gff3FeatureImpl region = new Gff3FeatureImpl("chr1", ".", "region", 1, 10000, -1d, Strand.NONE, -1, ImmutableMap.of("ID", Collections.singletonList("region01")));
+        final Gff3FeatureImpl feature1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "Parent", Collections.singletonList("region01")));
         feature1.addParent(region);
-        final Gff3FeatureImpl feature2 = new Gff3FeatureImpl("chr1", ".", "gene", 1300, 1600, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01", "Parent", "region01"));
+        final Gff3FeatureImpl feature2 = new Gff3FeatureImpl("chr1", ".", "gene", 1300, 1600, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "Parent", Collections.singletonList("region01")));
         feature2.addParent(region);
-        final Gff3FeatureImpl feature3 = new Gff3FeatureImpl("chr1", ".", "gene", 1700, 1900, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01", "Parent", "region01"));
+        final Gff3FeatureImpl feature3 = new Gff3FeatureImpl("chr1", ".", "gene", 1700, 1900, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "Parent", Collections.singletonList("region01")));
         feature3.addParent(region);
 
         feature1.addCoFeature(feature2);
@@ -128,11 +128,11 @@
 
     @Test(expectedExceptions = TribbleException.class)
     public void testCofeautresDifferentParents() {
-        final Gff3FeatureImpl feature1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene01"));
-        final Gff3FeatureImpl feature2 = new Gff3FeatureImpl("chr1", ".", "gene", 1300, 1600, Strand.NEGATIVE, -1, ImmutableMap.of("ID", "gene02"));
-        final Gff3FeatureImpl feature3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene01"));
+        final Gff3FeatureImpl feature1 = new Gff3FeatureImpl("chr1", ".", "gene", 1000, 1200, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01")));
+        final Gff3FeatureImpl feature2 = new Gff3FeatureImpl("chr1", ".", "gene", 1300, 1600, -1d, Strand.NEGATIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene02")));
+        final Gff3FeatureImpl feature3 = new Gff3FeatureImpl("chr1", ".", "CDS", 1010, 1050, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene01")));
         feature3.addParent(feature1);
-        final Gff3FeatureImpl feature4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1310, 1350, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "cds01","Parent", "gene02"));
+        final Gff3FeatureImpl feature4 = new Gff3FeatureImpl("chr1", ".", "CDS", 1310, 1350, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"),"Parent", Collections.singletonList("gene02")));
         feature4.addParent(feature2);
 
         //should throw exception because feature3 and feature4 have different parents so should not be co-features
@@ -144,7 +144,7 @@
 
         final int nGenerations = 10;
 
-        final Gff3FeatureImpl topLevelFeature = new Gff3FeatureImpl("chrX", ".", "type0", 1, 100, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "feature0"));
+        final Gff3FeatureImpl topLevelFeature = new Gff3FeatureImpl("chrX", ".", "type0", 1, 100, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("feature0")));
         Gff3FeatureImpl prevFeature = topLevelFeature;
 
         final Map<Gff3FeatureImpl, Set<Gff3FeatureImpl>> ancestorsMap = new HashMap<>();
@@ -156,7 +156,7 @@
         final List<Gff3FeatureImpl> features = new ArrayList<>(Arrays.asList(topLevelFeature));
 
         for (int i=1; i<nGenerations; i++) {
-            final Gff3FeatureImpl newFeature = new Gff3FeatureImpl("chrX", ".", "type" + i, 1, 100, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "feature" + i, "Parent", prevFeature.getID()));
+            final Gff3FeatureImpl newFeature = new Gff3FeatureImpl("chrX", ".", "type" + i, 1, 100, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("feature" + i), "Parent", Collections.singletonList(prevFeature.getID())));
             newFeature.addParent(prevFeature);
             ancestorsMap.put(newFeature, new HashSet<>(ancestorsMap.get(prevFeature)));
             ancestorsMap.get(newFeature).add(prevFeature);
@@ -179,13 +179,13 @@
     public void testFlatten() {
         final int nGenerations = 10;
 
-        final Gff3FeatureImpl topLevelFeature = new Gff3FeatureImpl("chrX", ".", "type0", 1, 100, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "feature0"));
+        final Gff3FeatureImpl topLevelFeature = new Gff3FeatureImpl("chrX", ".", "type0", 1, 100, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("feature0")));
         Gff3FeatureImpl prevFeature = topLevelFeature;
 
         final Map<Gff3FeatureImpl, Set<Gff3FeatureImpl>> flattenMap = new HashMap<>(Collections.singletonMap(topLevelFeature, new HashSet<>(Collections.singleton(topLevelFeature))));
 
         for (int i=1; i<nGenerations; i++) {
-            final Gff3FeatureImpl newFeature = new Gff3FeatureImpl("chrX", ".", "type" + i, 1, 100, Strand.NEGATIVE, 0, ImmutableMap.of("ID", "feature" + i, "Parent", prevFeature.getID()));
+            final Gff3FeatureImpl newFeature = new Gff3FeatureImpl("chrX", ".", "type" + i, 1, 100, -1d, Strand.NEGATIVE, 0, ImmutableMap.of("ID", Collections.singletonList("feature" + i), "Parent", Collections.singletonList(prevFeature.getID())));
             newFeature.addParent(prevFeature);
             flattenMap.forEach((k, v) -> v.add(newFeature));
             flattenMap.put(newFeature, new HashSet<>(Collections.singleton(newFeature)));
@@ -197,22 +197,22 @@
 
     @Test
     public void testDerivesFrom() {
-        final Gff3FeatureImpl region01 = new Gff3FeatureImpl("chrX", ".", "gene", 65, 1000, Strand.POSITIVE, -1, ImmutableMap.of("ID", "region01"));
+        final Gff3FeatureImpl region01 = new Gff3FeatureImpl("chrX", ".", "gene", 65, 1000, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("region01")));
 
-        final Gff3FeatureImpl gene01 = new Gff3FeatureImpl("chrX", ".", "gene", 1, 35, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene01", "Parent", "region01"));
+        final Gff3FeatureImpl gene01 = new Gff3FeatureImpl("chrX", ".", "gene", 1, 35, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "Parent", Collections.singletonList("region01")));
         gene01.addParent(region01);
-        final Gff3FeatureImpl gene02 = new Gff3FeatureImpl("chrX", ".", "gene", 70, 100, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene02"));
+        final Gff3FeatureImpl gene02 = new Gff3FeatureImpl("chrX", ".", "gene", 70, 100, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene02")));
 
-        final Gff3FeatureImpl mRNA01 = new Gff3FeatureImpl("chrX", ".", "mRNA", 1, 100, Strand.POSITIVE, -1 , ImmutableMap.of("ID", "mRNA01", "Parent", "gene01, gene02"));
+        final Gff3FeatureImpl mRNA01 = new Gff3FeatureImpl("chrX", ".", "mRNA", 1, 100, -1d, Strand.POSITIVE, -1 , ImmutableMap.of("ID", Collections.singletonList("mRNA01"), "Parent", Arrays.asList("gene01", "gene02")));
         mRNA01.addParent(gene01);
         mRNA01.addParent(gene02);
 
-        final Gff3FeatureImpl cds01 = new Gff3FeatureImpl("chrX", ".", "CDS", 1, 35, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds01", "Parent", "mRNA01", "Derives_from", "gene01"));
+        final Gff3FeatureImpl cds01 = new Gff3FeatureImpl("chrX", ".", "CDS", 1, 35, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds01"), "Parent", Collections.singletonList("mRNA01"), "Derives_from", Collections.singletonList("gene01")));
         cds01.addParent(mRNA01);
-        final Gff3FeatureImpl cds02 = new Gff3FeatureImpl("chrX", ".", "CDS", 70, 100, Strand.POSITIVE, 0, ImmutableMap.of("ID", "cds02", "Parent", "mRNA01", "Derives_from", "gene02"));
+        final Gff3FeatureImpl cds02 = new Gff3FeatureImpl("chrX", ".", "CDS", 70, 100, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("cds02"), "Parent", Collections.singletonList("mRNA01"), "Derives_from", Collections.singletonList("gene02")));
         cds02.addParent(mRNA01);
 
-        final Gff3FeatureImpl codon01 = new Gff3FeatureImpl("chrX", ".", "codon", 1, 3, Strand.POSITIVE, 0, ImmutableMap.of("ID", "codon01", "Parent", "cds01"));
+        final Gff3FeatureImpl codon01 = new Gff3FeatureImpl("chrX", ".", "codon", 1, 3, -1d, Strand.POSITIVE, 0, ImmutableMap.of("ID", Collections.singletonList("codon01"), "Parent", Collections.singletonList("cds01")));
         codon01.addParent(cds01);
 
         Assert.assertEquals(cds01.getAncestors(), ImmutableSet.of(mRNA01, gene01, region01));
@@ -232,12 +232,12 @@
 
     @Test
     public void testFeatureWithUnLoadedParent() {
-        final Gff3FeatureImpl gene01 = new Gff3FeatureImpl("chrX", ".", "gene", 1, 35, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene01", "Parent", "region01"));
-        final Gff3FeatureImpl gene02 = new Gff3FeatureImpl("chrX", ".", "gene", 1, 35, Strand.POSITIVE, -1, ImmutableMap.of("ID", "gene01", "Parent", "region01"));
+        final Gff3FeatureImpl gene01 = new Gff3FeatureImpl("chrX", ".", "gene", 1, 35, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "Parent", Collections.singletonList("region01")));
+        final Gff3FeatureImpl gene02 = new Gff3FeatureImpl("chrX", ".", "gene", 1, 35, -1d, Strand.POSITIVE, -1, ImmutableMap.of("ID", Collections.singletonList("gene01"), "Parent", Collections.singletonList("region01")));
 
         Assert.assertEquals(gene01, gene02);
 
-        final Gff3FeatureImpl mRNA01 = new Gff3FeatureImpl("chrX", ".", "mRNA", 1, 100, Strand.POSITIVE, -1 , ImmutableMap.of("ID", "mRNA01", "Parent", "gene01, gene02"));
+        final Gff3FeatureImpl mRNA01 = new Gff3FeatureImpl("chrX", ".", "mRNA", 1, 100, -1d, Strand.POSITIVE, -1 , ImmutableMap.of("ID", Collections.singletonList("mRNA01"), "Parent", Arrays.asList("gene01", "gene02")));
         mRNA01.addParent(gene01);
 
         Assert.assertNotEquals(gene01, gene02);
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3WriterTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3WriterTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3WriterTest.java	1970-01-01 00:00:00.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/tribble/gff/Gff3WriterTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -0,0 +1,205 @@
+package htsjdk.tribble.gff;
+
+import com.google.common.collect.ImmutableMap;
+import htsjdk.HtsjdkTest;
+import htsjdk.samtools.util.IOUtil;
+import htsjdk.tribble.AbstractFeatureReader;
+import htsjdk.tribble.TestUtils;
+import htsjdk.tribble.TribbleException;
+import htsjdk.tribble.readers.LineIterator;
+import org.testng.Assert;
+import org.testng.TestException;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.RandomAccessFile;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.zip.GZIPInputStream;
+
+public class Gff3WriterTest extends HtsjdkTest {
+    private final static String DATA_DIR = TestUtils.DATA_DIR + "/gff/";
+    private final Path ensembl_human_small = Paths.get(DATA_DIR + "Homo_sapiens.GRCh38.97.chromosome.1.small.gff3");
+    private final Path gencode_mouse_small = Paths.get(DATA_DIR + "gencode.vM22.annotation.small.gff3");
+    private final Path ncbi_woodpecker_small = Paths.get(DATA_DIR + "ref_ASM69900v1_top_level.small.gff3");
+    private final Path feature_extends_past_circular_region = Paths.get(DATA_DIR + "feature_extends_past_circular_region.gff3");
+    private final Path with_fasta = Paths.get(DATA_DIR + "fasta_test.gff3");
+    private final Path with_fasta_artemis = Paths.get(DATA_DIR + "fasta_test_artemis.gff3");
+    private final Path ordered_cofeature = Paths.get(DATA_DIR, "ordered_cofeatures.gff3");
+    private final Path child_before_parent = Paths.get(DATA_DIR, "child_before_parent.gff3");
+    private final Path url_encoding = Paths.get(DATA_DIR, "url_encoding.gff3");
+    private final static Path[] tmpDir = new Path[] {IOUtil.getDefaultTmpDirPath()};
+    private final static String version3Directive = "##gff-version 3.1.25\n";
+
+    @DataProvider(name = "roundTripDataProvider")
+    public Object[][] roundTripDataProvider() {
+        return new Object[][] {
+                {ensembl_human_small}, {gencode_mouse_small}, {ncbi_woodpecker_small}, {feature_extends_past_circular_region}, {with_fasta}, {with_fasta_artemis},
+                {ordered_cofeature}, {child_before_parent}, {url_encoding}
+        };
+    }
+
+    @Test(dataProvider = "roundTripDataProvider")
+    public void testRoundTrip(final Path path) {
+
+        final List<String> comments1 = new ArrayList<>();
+        final HashSet<SequenceRegion> regions1 = new HashSet<>();
+        final LinkedHashSet<Gff3Feature> features1 = readFromFile(path, comments1, regions1);
+
+            //write out to temp files (one gzipped, on not)
+        try {
+            final Path tempFile = IOUtil.newTempPath("gff3Writer", ".gff3", tmpDir);
+            final Path tempFileGzip = IOUtil.newTempPath("gff3Writer", ".gff3.gz", tmpDir);
+
+            writeToFile(tempFile, comments1, regions1, features1);
+            writeToFile(tempFileGzip, comments1, regions1, features1);
+
+            //read temp files back in
+
+            Assert.assertTrue(isGZipped(tempFileGzip.toFile()));
+            final List<String> comments2 = new ArrayList<>();
+            final HashSet<SequenceRegion> regions2 = new HashSet<>();
+            final LinkedHashSet<Gff3Feature> features2 = readFromFile(tempFile, comments2, regions2);
+
+
+            final List<String> comments3 = new ArrayList<>();
+            final HashSet<SequenceRegion> regions3 = new HashSet<>();
+            final LinkedHashSet<Gff3Feature> features3 = readFromFile(path, comments3, regions3);
+
+            Assert.assertEquals(features1, features2);
+            Assert.assertEquals(features1, features3);
+
+            Assert.assertEquals(comments1, comments2);
+            Assert.assertEquals(comments1, comments3);
+            Assert.assertEquals(regions1, regions2);
+            Assert.assertEquals(regions1, regions3);
+        } catch (final IOException ex) {
+            throw new TribbleException("Error creating temp files", ex);
+        }
+    }
+
+    private void writeToFile(final Path path, final List<String> comments, final Set<SequenceRegion> regions, final Set<Gff3Feature> features) {
+        try (final Gff3Writer writer = new Gff3Writer(path)) {
+            for (final String comment : comments) {
+                writer.addComment(comment);
+            }
+
+            for (final SequenceRegion region : regions) {
+                writer.addDirective(Gff3Codec.Gff3Directive.SEQUENCE_REGION_DIRECTIVE, region);
+            }
+
+            for (final Gff3Feature feature : features) {
+                writer.addFeature(feature);
+            }
+        } catch (final IOException ex) {
+            throw new TribbleException("Error writing to file " + path, ex);
+        }
+    }
+
+    private LinkedHashSet<Gff3Feature> readFromFile(final Path path, List<String> commentsStore, Set<SequenceRegion> regionsStore) {
+        final Gff3Codec codec = new Gff3Codec();
+        final LinkedHashSet<Gff3Feature> features = new LinkedHashSet<>();
+        try (final AbstractFeatureReader<Gff3Feature, LineIterator> reader = AbstractFeatureReader.getFeatureReader(path.toAbsolutePath().toString(), null, codec, false)) {
+            for (final Gff3Feature feature : reader.iterator()) {
+                features.add(feature);
+            }
+
+            commentsStore.addAll(codec.getCommentTexts());
+            regionsStore.addAll(codec.getSequenceRegions());
+        } catch (final IOException ex) {
+            throw new TribbleException("Error reading gff3 file " + path);
+        }
+
+        return features;
+    }
+
+    @DataProvider(name = "writeKeyValuePairDataProvider")
+    public Object[][] writeKeyValuePairDataProvider() {
+        return new Object[][] {
+                {"key",Arrays.asList("value1", "value2", "value3"), "key=value1,value2,value3"},
+                {"key",Arrays.asList("value1", "value ; with = special & encoded , characters", "value3"), "key=value1,value %3B with %3D special %26 encoded %2C characters,value3"}
+        };
+    }
+
+    @Test(dataProvider = "writeKeyValuePairDataProvider")
+    public void testWriteKeyValuePair(final String key, final List<String> values, final String expectedOutput) {
+        final ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+        try(final Gff3Writer writer = new Gff3Writer(outputStream)) {
+            writer.writeKeyValuePair(key, values);
+        } catch (final IOException ex) {
+            throw new TestException("Error writing key value pair", ex);
+        }
+
+        final byte[] expectedBytes = (version3Directive + expectedOutput).getBytes();
+
+        Assert.assertEquals(outputStream.toByteArray(), expectedBytes);
+    }
+
+    @DataProvider(name = "writeAttributesDataProvider")
+    public Object[][] writeAttributesDataProvider() {
+        return new Object[][] {
+                {ImmutableMap.of("key1", Arrays.asList("value1", "value2"), "key2", Collections.singletonList("another value"), "key3", Arrays.asList("thisValue")),
+                "key1=value1,value2;key2=another value;key3=thisValue"},
+                {ImmutableMap.of("singleKey", Arrays.asList("multipleValue1", "multipleValue2")), "singleKey=multipleValue1,multipleValue2"},
+                {ImmutableMap.of("singleKey", Collections.singletonList("singleValue")), "singleKey=singleValue"},
+                {Collections.emptyMap(), "."}
+        };
+    }
+
+    @Test(dataProvider = "writeAttributesDataProvider")
+    public void testWriteAttributes(final Map<String, List<String>> attributes, final String expectedOutput) {
+        final ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+        try(final Gff3Writer writer = new Gff3Writer(outputStream)) {
+            writer.writeAttributes(attributes);
+        } catch (final IOException ex) {
+            throw new TestException("Error writing key value pair", ex);
+        }
+
+        final byte[] expectedBytes = (version3Directive + expectedOutput).getBytes();
+
+        Assert.assertEquals(outputStream.toByteArray(), expectedBytes);
+    }
+
+    @DataProvider(name = "encodeStringDataProvider")
+    public Object[][] encodeStringDataProvider() {
+        return new Object[][] {
+                {"%", "%25"},
+                {";", "%3B"},
+                {"=", "%3D"},
+                {"&", "%26"},
+                {",", "%2C"},
+                {" ", " "},
+                {"qwertyuiopasdfghjklzxcvbnmQWERTYUIOPASDFGHJKLZXCVBNM ", "qwertyuiopasdfghjklzxcvbnmQWERTYUIOPASDFGHJKLZXCVBNM "} //these should remain unchanged
+        };
+    }
+
+    @Test(dataProvider = "encodeStringDataProvider")
+    public void testEncodeString(final String decoded, final String expectedEncoded) {
+        final String encoded = Gff3Writer.encodeString(decoded);
+
+        Assert.assertEquals(encoded, expectedEncoded);
+    }
+
+    private static boolean isGZipped(final File f) {
+        int magic = 0;
+        try {
+            RandomAccessFile raf = new RandomAccessFile(f, "r");
+            magic = raf.read() & 0xff | ((raf.read() << 8) & 0xff00);
+            raf.close();
+        } catch (Throwable e) {
+            e.printStackTrace(System.err);
+        }
+        return magic == GZIPInputStream.GZIP_MAGIC;
+    }
+}
\ No newline at end of file
diff -Nru htsjdk-2.22.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java
--- htsjdk-2.22.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java	2020-07-08 16:28:01.000000000 +0000
@@ -3,6 +3,9 @@
 import com.google.common.jimfs.Configuration;
 import com.google.common.jimfs.Jimfs;
 import htsjdk.HtsjdkTest;
+import htsjdk.samtools.seekablestream.SeekableStream;
+import htsjdk.samtools.seekablestream.SeekableStreamFactory;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.tribble.TestUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
@@ -12,6 +15,7 @@
 import java.io.IOException;
 import java.nio.file.FileSystem;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -97,4 +101,29 @@
         // fail if a test that should have thrown didn't
         Assert.assertTrue(shouldSucceed, "Test should have failed but succeeded");
     }
+
+    @Test
+    public void testTabixFileWithEmbeddedSpaces() throws IOException {
+        final File testVCF =  new File(TEST_DATA_DIR, "HiSeq.10000.vcf.bgz");
+        final File testTBI =  new File(TEST_DATA_DIR, "HiSeq.10000.vcf.bgz.tbi");
+
+        // Copy the input files into a temporary directory with embedded spaces in the name.
+        // This test needs to include the associated .tbi file because we want to force execution
+        // of the tabix code path.
+        final File tempDir = IOUtil.createTempDir("test spaces", "");
+        Assert.assertTrue(tempDir.getAbsolutePath().contains(" "));
+        tempDir.deleteOnExit();
+        final File inputVCF = new File(tempDir, "HiSeq.10000.vcf.bgz");
+        inputVCF.deleteOnExit();
+        final File inputTBI = new File(tempDir, "HiSeq.10000.vcf.bgz.tbi");
+        inputTBI.deleteOnExit();
+        IOUtil.copyFile(testVCF, inputVCF);
+        IOUtil.copyFile(testTBI, inputTBI);
+
+        try (final VCFFileReader vcfFileReader = new VCFFileReader(inputVCF)) {
+            Assert.assertNotNull(vcfFileReader.getFileHeader());
+        }
+
+    }
+
 }
diff -Nru htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/samtools/util/sliver.sam htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/util/sliver.sam
--- htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/samtools/util/sliver.sam	1970-01-01 00:00:00.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/util/sliver.sam	2020-07-08 16:28:01.000000000 +0000
@@ -0,0 +1,120 @@
+@HD	VN:1.5	GO:query	SO:coordinate
+@SQ	SN:chr1	LN:248956422	AS:38	M5:6aef897c3d6ff0c78aff06ac189178dd	UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta	SP:Homo sapiens
+@RG	ID:HJYFJ.4	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HJYFJCCXX160204.4.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HJYFJ.5	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HJYFJCCXX160204.5.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HJYFJ.6	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HJYFJCCXX160204.6.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HJYFJ.7	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HJYFJCCXX160204.7.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HJYFJ.8	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HJYFJCCXX160204.8.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HJYN2.1	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HJYN2CCXX160123.1.TATCCAGG	CN:BI	DT:2016-01-23T00:00:00-0500	PI:0
+@RG	ID:HK35M.1	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.1.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.2	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.2.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.3	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.3.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.4	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.4.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.5	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.5.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.6	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.6.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.7	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.7.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35M.8	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35MCCXX160204.8.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35N.1	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35NCCXX160204.1.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK35N.2	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK35NCCXX160204.2.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.1	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.1.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.2	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.2.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.3	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.3.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.4	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.4.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.5	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.5.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.6	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.6.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.7	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.7.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HK3T5.8	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HK3T5CCXX160204.8.TATCCAGG	CN:BI	DT:2016-02-04T00:00:00-0500
+@RG	ID:HM3G2.2	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HM3G2CCXX160308.2.TATCCAGG	CN:BI	DT:2016-03-08T00:00:00-0500
+@RG	ID:HTL2K.5	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HTL2KCCXX160412.5.TATCCAGG-GAAGTGGA	CN:BI	DT:2016-04-12T00:00:00-0400
+@RG	ID:HTL2K.6	SM:NA12891	LB:Pond-492101	PL:illumina	PU:HTL2KCCXX160412.6.TATCCAGG-GAAGTGGA	CN:BI	DT:2016-04-12T00:00:00-0400
+@PG	ID:bwamem	VN:0.7.15-r1140	CL:bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta	PN:bwamem
+@PG	ID:MarkDuplicates	VN:2.22.3-SNAPSHOT	CL:MarkDuplicates CLEAR_DT=false ADD_PG_TAG_TO_READS=false INPUT=[/cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-0/HJYFJCCXX.4.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-1/attempt-2/HJYFJCCXX.5.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-2/HJYFJCCXX.6.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-3/HJYFJCCXX.7.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-4/HJYFJCCXX.8.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-5/HJYN2CCXX.1.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-6/HK35MCCXX.1.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-7/attempt-2/HK35MCCXX.2.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-8/HK35MCCXX.3.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-9/attempt-2/HK35MCCXX.4.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-10/HK35MCCXX.5.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-11/HK35MCCXX.6.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-12/HK35MCCXX.7.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-13/HK35MCCXX.8.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-14/HK35NCCXX.1.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-15/HK35NCCXX.2.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-16/HK3T5CCXX.1.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-17/HK3T5CCXX.2.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-18/attempt-2/HK3T5CCXX.3.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-19/HK3T5CCXX.4.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-20/HK3T5CCXX.5.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-21/HK3T5CCXX.6.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-22/attempt-2/HK3T5CCXX.7.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-23/HK3T5CCXX.8.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SplitRG/shard-24/SplitLargeReadGroup/49809670-d61e-402a-b77d-153e60fced2c/call-GatherMonolithicBamFile/HM3G2CCXX.2.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-25/HTL2KCCXX.5.Pond-492101.aligned.unsorted.bam, /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/ea7f25d6-e4fd-4b5a-922b-275d6a0c77e6/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/9c5cdb6a-911d-42cb-ace2-33dc123a2cac/call-SamToFastqAndBwaMemAndMba/shard-26/attempt-2/HTL2KCCXX.6.Pond-492101.aligned.unsorted.bam] OUTPUT=NA12891.aligned.unsorted.duplicates_marked.bam METRICS_FILE=NA12891.duplicate_metrics ASSUME_SORT_ORDER=queryname OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 VALIDATION_STRINGENCY=SILENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false	PN:MarkDuplicates
+@PG	ID:GATK ApplyBQSR	VN:4.1.7.0-11-gee56f27-SNAPSHOT	CL:ApplyBQSR  --output NA12891.aligned.duplicates_marked.recalibrated.bam --bqsr-recal-file /cromwell_root/broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/75ae53b9-3b67-4ec8-88af-2dffc4704879/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/e51137c1-0348-4b13-9a93-557fdb7073db/call-GatherBqsrReports/NA12891.recal_data.csv --use-original-qualities true --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 --intervals chr1:1+ --input gs://broad-gotc-dev-cromwell-execution/WholeGenomeGermlineSingleSample/75ae53b9-3b67-4ec8-88af-2dffc4704879/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/e51137c1-0348-4b13-9a93-557fdb7073db/call-SortSampleBam/NA12891.aligned.duplicate_marked.sorted.bam --reference /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta --create-output-bam-md5 true --add-output-sam-program-record true  --preserve-qscores-less-than 6 --quantize-quals 0 --round-down-quantized false --emit-original-quals false --global-qscore-prior -1.0 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false	PN:GATK ApplyBQSR
+@PG	ID:GATK PrintReads	VN:4.0.11.0-13-g36f4305-SNAPSHOT	CL:PrintReads  --output sliver.bam --intervals chr1:781443-790000 --intervals chr1:790000-790478 --input /seq/tng/ggrant/Support/GL-744/NA12891.bam  --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false	PN:GATK PrintReads
+HK35MCCXX160204:5:1107:6340:34799	99	chr1	787876	60	151M	=	787997	272	TTTCTACTCCACTATTCTATCATGGTGCATTTTAGGTGCTAATGGGAAAATCTGCTCTATGATGGTGTCCAATAGACAATTAAAATTCAAATCTGGAGATGAGATCTGGACTGAAGATTTTTTTAAAAATTAGCCCTCATCACATGTAGTC	??????5??5?5?+??????????5+'??????????????+5?????????????5?+????5?????'?????555?+??5????+???++????'?+??55+5??5????????++?????5???5++5+'?55'5?555?+??????	MC:Z:151M	RG:Z:HK35M.5	MQ:i:50	AS:i:146
+HK3T5CCXX160204:7:1212:23267:47492	147	chr1	788025	48	151M	=	787983	-193	TCAGCTGTAGAAATCCTTAGCATGGCTGAAATTTTTCATATTAAGACAAGACTAGAACTTGGCCAGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGTGAATCACCTGAGGTCTGGAGTTTGAGACCAGCTG	????????5?????????????????????????????????????????????????????5????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HK3T5.7	MQ:i:60	AS:i:151
+HK35NCCXX160204:1:2218:30391:4034	147	chr1	788028	47	151M	=	787976	-203	GCTGTAGAAATCCTTAGCATGGCTGAAATGTTTCATATTAAGACAAGACTAGAACTTGGCCAGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGTGAATCACCTGAGGTCTGGAGTTTGAGACCAGCTGACC	?????????5???????????????????'?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????5???	MC:Z:151M	RG:Z:HK35N.1	MQ:i:60	AS:i:146
+HK35MCCXX160204:2:1206:26555:70768	99	chr1	788175	48	151M	=	788302	275	GACCAACATGGTGAAACACCATCTCTACTAAAAATACAAAAAATTAGCCAGGCGTGGTTGCACATGCCTGTAATCCTAGCTACTTGGGAAGCTGAGGTAGGAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGCAAGCTGAGATCGTGC	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????5?????5?????????5???????????	MC:Z:5S117M2D29M	RG:Z:HK35M.2	MQ:i:60	AS:i:151
+HTL2KCCXX160412:5:2211:10044:18854	147	chr1	788179	45	151M	=	788003	-327	AGCATGGTGAAACACCATCTCGACGAAAAATACAAAAAATTAGCCAGGCGTGGTTGCACATGCCTGTAATCCTAGCTACTTGGGAAGCTGAGGGAGGAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGCAAGCTGAGATCGTGCCATT	###############################################???????????+?????????5???????5?++5???5??5?????'??????????????5555???????????????????????????????????????	MC:Z:151M	RG:Z:HTL2K.5	MQ:i:47	AS:i:134
+HK35MCCXX160204:7:2201:4350:10925	147	chr1	788265	60	151M	=	787867	-549	GCTGAGGCGGGAGAATTCATTGAAACCAGGGGGTGGAGGTTGCAGCACGCTGAGATCGTGCCATTGCACTGCAGTCTGGGCAAAAAAAGCAAAACTCTGAAGAAAGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGAGGAGA	###############################??????????5+5??+%?5?????55???'5+??5+?5?????55????5?????5?5??+5???????5????????????5??5????????????????????????5+5'?+??5+	MC:Z:151M	RG:Z:HK35M.7	MQ:i:60	AS:i:112
+HK3T5CCXX160204:3:2222:23226:52098	147	chr1	788330	60	89M2D62M	=	787951	-532	GCACGGCAGTCGGGGCAAAAAAAGCAAAGCGCTGAGGAAAGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGATGAGAGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATCGAGCAGGAA	######################################???????????5?5?????55???????????????????5????????????????????????????????????????????55????'???????5+????????????	MC:Z:151M	RG:Z:HK3T5.3	MQ:i:47	AS:i:118	CO:Z:needed
+HTL2KCCXX160412:5:2105:26463:13263	83	chr1	788340	60	79M2D72M	=	788051	-442	CTGGGCAAAAAAAGCAAAACTCTGAAGAAAGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGATGAGAGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATCGAGCAGGAACCTTGGAGGA	???????????5??5???+?55????????????55????????????????????????????????5????????????????????????????????????5?????????????????????????????????????????????	MC:Z:151M	RG:Z:HTL2K.5	MQ:i:47	AS:i:143	CO:Z:needed
+HTL2KCCXX160412:6:2222:7923:31670	99	chr1	788483	47	151M	=	788786	448	CCTTGGAGGACCTATTGCTTAAGGTGTGCGCCAAAGAAAGTAAGTTAGGGCAAGAGACTAAGGTATGCCAGAGACCCAGGACAAAACACAGTGCAGAGTGATGTCACAGAGCCAAATGGGAGTGCAAGCTATGGCAAGCCCTCCCAAGTAT	?????????????????????????????5????????????????????????????????????????????????????????????????????????????????????????????5????????????????????????????	MC:Z:6S145M	RG:Z:HTL2K.6	MQ:i:60	AS:i:146
+HM3G2CCXX160308:2:2202:10906:14055	147	chr1	788492	47	151M	=	788009	-634	ACCTATTGCTTAAGGTGTGCGCCAAAGAAAGTAAGTTAGGGCAAGAGACTAAGGTATGCCAGAGACCCAGGACAAAACACAGTGCAGAGTGATGTCACAGAGCCAAATGGGAGTGCAAGCTATGGCAAGCCCTCCCAAGTATGTGTGGGTT	??55??????????5+'+?????????5??????????????????5?????5?????????????????????????????5?????5++55??????????????5????????????5???????????5?????????????????5	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:48	AS:i:146
+HM3G2CCXX160308:2:2204:20344:54559	83	chr1	788632	60	151M	=	788525	-258	ATGTGTGGGTTAAATGTAATTAAATTCAAAATCTCTCAACCCAAAAATTTTCTCCACAAAGGAAGTAGAGAAACAAAACAGTTCATTATTGAATAAGCATTAAACCAGAATGTGATGTGTGAATATAATGGAATGGAATGGAATGGAATGG	?????5?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:48	AS:i:151
+HTL2KCCXX160412:5:2114:28970:33533	83	chr1	788634	60	151M	=	788475	-310	GTGTGGGTTAAATGTAATTAAATTCAAAATCTCTCAACCCAAAAATTTTCTCCACAAAGGAAGTAGAGAAACAAAACAGTTCATTATTGAATAAGCATTAAACCAGAATGTGATGTGTGAATATAATGGAATGGAATGGAATGGAATGGAA	5??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HTL2K.5	MQ:i:47	AS:i:151
+HM3G2CCXX160308:2:1112:23947:64316	147	chr1	788638	60	151M	=	788512	-277	GGGTTAAATGTAATTAAATTCAAAATCTCTCAACCCAAAAATTTTCTCCACAAAGGAAGTAGAGAAACAAAACAGTTCATTATTGAATAAGCATTAAACCAGAATGTGATGTGTGAATATAATGGAATGGAATGGAATGGAATGGAATGGA	5???????5??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:57	AS:i:151
+HTL2KCCXX160412:5:1203:20730:58005	163	chr1	788659	60	151M	=	789197	689	AAAATCTCTCAACCCAAAAATTTTCTCCACAAAGGAAGTAGAGAAACAAAACAGTTCATTATTGAATAAGCATTAAACCAGAATGTGATGTGTGAATATAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAA	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????5+5??	MC:Z:151M	RG:Z:HTL2K.5	MQ:i:59	AS:i:150
+HTL2KCCXX160412:6:2222:7923:31670	147	chr1	788786	60	6S145M	=	788483	-448	AGGAGGGGAATGGAATGGAATGGAATGGAGTGGGGTGGAATGGACCCGAATGGAATGGGACGGAACGGAATGGAATGGAACGCACTCGAATGGAATGGAACGGACATGAATGGAATGGAATGGAACGGACACGAATGGAACGGAACGGAAC	################?+????55?5??5555++55??55???5+?5??????5?5??'?????????????????????5?55??5???????????5?5??????????????????????????????5????????5????5?????	MC:Z:151M	RG:Z:HTL2K.6	MQ:i:47	AS:i:135
+HM3G2CCXX160308:2:2210:12611:69607	145	chr1	788787	0	30S38M83S	=	104086	0	GAATGGAGTAGAGTGAGATGAAATGAAATAGAATGGAATGGAATGGAACGGAGTGGAGTGGAATGGACATGAGTGGAGTTGACTGGAGTGGAACGGAGTGCAGGGGAAAGGAATGGTATAGATTGGNATTGAATGTAATGGAATGGAGTGG	???????????5?5?5??+?5????5???5?5?555?????55?????5???????????????????????????????????????5???????????+?????????????????????????#????????????????????????	SA:Z:chrUn_KI270589v1,44033,+,46S55M50S,0,5;	MC:Z:15M6D73M5I31M27S	RG:Z:HM3G2.2	MQ:i:4	AS:i:33
+HM3G2CCXX160308:2:2203:16427:24181	163	chr1	788788	60	147M4S	=	789217	580	AATGGAATGGAATGGAATGGAGTGGAGTGGAGTGGACCGGAATGGAATGGAACGGAACGGAATGGAATGGAACGGACTCGAATGGAATGGAACGGAAAGGAATGGCATGGAATGGAACGGACTGGAATGGAACGGGAAGGAACGGAAAGGG	???????????????????????????????+5?5??+&+?+???5+5++5++5+??&&??5?????5????+5++'?5?5?55??+5????###########################################################	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:97
+HK3T5CCXX160204:4:2104:3194:19118	163	chr1	788792	60	108M43S	=	788987	347	GAATGGAATGGAATGGAGTGGAGTGGAATGGACCCGAATGGAATGGAACGGAACGGAATGGAATGGAACGCAATCGAGGGGAATGGAACGGAAAGGAATGGAATGGAAGGGAAGTGACGGGAAGTGAGGGGAGGGGAACGTAATGAATGTG	????????????????????????????????????????????????????????????????????????++'+?+5'&?5+????'5?############################################################	MC:Z:3M1D148M	RG:Z:HK3T5.4	MQ:i:60	AS:i:83
+HTL2KCCXX160412:6:2112:19816:65634	147	chr1	788923	60	151M	=	788531	-543	AACGGAACGGAATGGACTTGAGTGGGATGGAATGGAATTGAATGGACTCTAATGGAATGGACATGAATGGAATGGAATGGACTCAATTGGAATGCAGTTGAATTGAAAGGATCCAAAAGGAATGCAATGGAATGCATTGGAATGGAATGCA	??5????55??????5+????'5??????????5?????????????5?????????????????????????????????5??????????????5???????????????5?5????????5+??????????????????????????	MC:Z:151M	RG:Z:HTL2K.6	MQ:i:48	AS:i:151
+HK35MCCXX160204:4:2111:17716:35098	99	chr1	788932	60	71M80S	=	788932	71	GAATGGACTTGAGTGGGATGGAATGGAATTGAATGGACTCTAATGGAATGGACATGAATGGAATGGAATGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATCGAGGATCACGTATGCCGTCTTCTGCTGGAAGAAATGAAGGTG	???????????????????????????????????????????????????????????????????????????5%'55??+'55????+5+?????++?+5????############################################	MC:Z:80S71M	RG:Z:HK35M.4	MQ:i:60	AS:i:72	XT:i:72
+HK35MCCXX160204:3:2108:30573:38526	83	chr1	788932	60	151M	=	788685	-398	GAATGGACTGGGGTGGGATGGAATGGAATTGAATGGACTCTAAGGGAATGGAAATGAATGGAATGGAATGGGCTCAATTGGAATGCAGTTGAATTGAAAGGATCCAAAAGGAATGCAATGGAATGCATTGGAATGGAATGCAATGGACTTG	################################################################??+5???'55?????55+?+?5??+????5???+????????????55??55??+???????????????????????????????+	MC:Z:115M36S	RG:Z:HK35M.3	MQ:i:60	AS:i:126
+HK35MCCXX160204:4:2111:17716:35098	147	chr1	788932	60	80S71M	=	788932	-71	TATATTTTTTAATGATATGGCGACTAGCGAGATCTACACTCCACTTCACACTCTTTCCCTACGCGACGCTCTTCAGATCTGAATGGAGTTGAGTGGGATGGAATGGAATTGAATGGACTCTAATGGAATGGACATGAATGGAATGGAATGG	###########################??55????+5?????5???5+5+??+?5????5?%%$5+%5+?+55+55+5'????????&?????????????????????????????5?5???????????????????????????????	MC:Z:71M80S	RG:Z:HK35M.4	MQ:i:60	AS:i:66	XT:i:72
+HJYFJCCXX160204:7:2101:22110:38280	163	chr1	788933	58	151M	=	789379	569	AATGGACTTGAGTGGGATGGAATGGAATTGAATGGACTCTAATGGAATGGACATGAATGGAATGGAATGGACTCAATTGGAATGCAGTTGAATTGAAAGGATCCAAAAGGAATGCAATGGAATGCATTGGAATGGAATGCAATGGACTTGA	????????????????????????????????????????????????????????????????????????????????????'?????????????????'?????????????????????5?+??????????5?'??5???'?5??	MC:Z:123M28S	RG:Z:HJYFJ.7	MQ:i:53	AS:i:151
+HK35MCCXX160204:7:2109:16518:61995	163	chr1	788946	60	151M	=	789009	214	GGGATGGAATGGAATTGAATGGACTCTAATGGAATGGACATGAATGGAATGGAATGGACTCAATTGGAATGCAGTTGAATTGAAAGGATCCAAAAGGAATGCAATGGAATGCATTGGAATGGAATGCAATGGACTTGAATGGGATGGAATG	???????????????????????????????????????????????????????????????5??????????5??????????????????????????????????????????????????????????55?????????5?????5	MC:Z:151M	RG:Z:HK35M.7	MQ:i:60	AS:i:151
+HK3T5CCXX160204:4:2208:17208:11119	163	chr1	788946	45	151M	=	789266	471	GGGATGGAATGGAATTGAATGGACTCTAATGGAATGGACATGAATGGAATGGAATGGACTCAATTGGAATGCAGTTGAATTGAAAGGATCCAAAAGGAATGCAATGGAATGCATTGGAATGGAATGCAATGGAATGGAATGGGATGGAATG	?????????????????????????????????????????????????????????????5++??????????????????????????????????????????????????5?????5?????5??????555?5?5??5??+?####	MC:Z:151M	RG:Z:HK3T5.4	MQ:i:60	AS:i:141
+HTL2KCCXX160412:6:1219:25195:10152	83	chr1	789083	60	151M	=	788936	-298	AATGGGATGGAATGGAATGGAATGGACTCTAATGGAACGGAATGGAATGGAACCGAATGGAATGGAATGGACTTGAATGGAATAGAATGGAATGGAATGGACTCGAAAGAAATGAAATGGAATGGATTCAAATGGAATGGAATGGACACAA	###????55????????????????55?????????????5??????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HTL2K.6	MQ:i:60	AS:i:151
+HJYFJCCXX160204:7:1205:5203:35924	99	chr1	789086	60	151M	=	789187	245	GGGATGGAATGGAATGGAATGGACTCTAATGGAACGGAATGGAATGGAACCGAATGGAATGGAATGGACTTGAATGGAATAGAATGGAATGGAATGGACTCGAAAGAAATGAAATGGAATGGATTCAAATGGAATGGAATGGACACAAATG	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????+??????????????????????????	MC:Z:7S144M	RG:Z:HK3T5.1	MQ:i:45	AS:i:151
+HM3G2CCXX160308:2:1117:12865:16990	99	chr1	789235	21	77M5I69M	=	789666	503	TGGAACAGAATGGAATGGAAAGGACTCGAATAGAATACAATGGAATTTAATGGAATGGTCTCTAATGGAATGGAATGGAATAGACTAGAATGGTATGGAAGGGAATAGACTAGAGTGGAATGGAAGGCAATGGAATGGTCTCCAATTGAAT	???????????????????????????????????????????????????????????????????????????????????????????????????????+???????????5???????????????????????????????????	MC:Z:69S39M10I33M	RG:Z:HM3G2.2	MQ:i:21	AS:i:59
+HK35MCCXX160204:8:2202:18984:30158	83	chr1	789237	45	151M	=	788898	-490	GAACCAAATGGAATGGAATGGACTCGAATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGAATGGACTAGAATGGAATAGCACGGAATAGGCTCGAATGGTATGGAATGCAATGGAATGGACTCGAATGGAATAGAACAG	??????????????????????????????????????????????????????55?'+?++??????5?????????????5???????5'+5??????&?5++??????????5+??????????????????????????????????	MC:Z:28M123S	RG:Z:HK35M.8	MQ:i:45	AS:i:146
+HTL2KCCXX160412:6:1111:20740:62101	147	chr1	789237	60	151M	=	789136	-252	GAACCAAATGGAAGGGAAAGGACTCGAATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGAATGGACTAGAATGGAATAGAACGGAATAGGCTCGAATGGTATGGAATGCAATGGAATGGACTCGAATGGAATAGAACAG	#########################???55?????????55??????????????????????????????????????????????????+??????????????????????????????????????????5????????????????	MC:Z:149M2S	RG:Z:HTL2K.6	MQ:i:60	AS:i:141
+HM3G2CCXX160308:2:2213:9557:38965	147	chr1	789238	59	151M	=	789076	-313	AAACAAATGGAATGGAATGGACTCGTATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGCATTGACTAGAATGGAATAGAACGGAATAGGCTCGAATGGTATGGAATGCAATGGANTGGACTCGAATGGAATAGAACAGA	?55???????????????????+'5'?5++55'5+5?+5?????5????????55??55'5++????5?5+??+?????5??++5?????????+????????5??????'????????5??????#????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:131
+HTL2KCCXX160412:6:2205:10145:11189	99	chr1	789239	9	151M	=	789681	493	ACCAAATGGAATGGAATGGACTCGAATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGAATGGAATAGAACGGAATAGAACGGAATAGACTCGAATGGAATGGAACTGAAAGGAATTGAATCGAATGGAATAGAACAGAA	??????????????????????55????????5????????????????????????55???????5????55??5?????+&??????555&?5?55+?&?55??5??##########################################	MC:Z:91S51M9S	RG:Z:HTL2K.6	MQ:i:9	AS:i:101
+HM3G2CCXX160308:2:1104:29011:27486	83	chr1	789240	60	151M	=	789106	-285	CCAAATGGAATGGAATGGACTCGAATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGAATGGACTAGAATGGAATAGAACGGAATAGGCTCGAATGGTATGGAATGCAATGGAATGGACTCGAATGGAATAGAACAGAAT	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:151
+HK3T5CCXX160204:5:2207:25175:46402	83	chr1	789290	60	151M	=	788937	-504	TGGACTCAAATTGAAAGGAATGGACTAGAATGGAACAGAACGGAATTGGCTCGAATGGTATGGAATGCAATGGAATGGACTCGAATGGAATAGAACAGAATAGACTAGAATGGTATGGAATGCAATGTAATGGACTCGAATGGAACGGAAT	#############################?????5++5??55????+????$'+5?????????????????????5'+'+$???????5?????'?'++????????????5?????????????55?????????????????"?????	MC:Z:97M54S	RG:Z:HK3T5.5	MQ:i:59	AS:i:126
+HM3G2CCXX160308:2:1122:25804:7726	83	chr1	789356	60	146M5S	=	789229	-273	GCAATGGAATGGACTCGAATGGAATAGAACAGGATAGACTAGTATGGTATGGAATGCAATGTAATGGACTCGAATGGAACGGAATGGAATGGACAAGAATTGAATTGAATGGACTGGAATGGAATGGAATGGAATGCAATGGAATGCACTC	?????+????+??++???????????+55+?++5'?55+55''?+5$'???5??55+????'???+??'?5???55???'???5+5???????5??+?????????5???+5?????????????55???5?????????5????+?????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:59	AS:i:126
+HTL2KCCXX160412:6:1212:28929:37366	97	chr1	789385	47	117M34S	=	16360682	0	CAGAATAGACTAGAATGGTATGGAATGCAATGTAATGGACTCGAATGGAACGGAATGGAATGGACAAGAATTGAATTGAATGGACTGGAATGGAATGGAATGGAATGCAATGGAATGCACTCGAACGGATTGGAATGGAATGGACTCGAAT	??????????????????????????????????????????5???????????????????????????????????????????????????????????????????????????????????????????????????????????#	SA:Z:chrUn_GL000216v2,65758,-,58M93S,0,4;	MC:Z:90M1I60M	RG:Z:HTL2K.6	MQ:i:13	AS:i:107
+HTL2KCCXX160412:6:1217:9485:17149	129	chr1	789385	58	104M47S	=	24814	0	CAGAATAGACTAGAATGGTATGGAATGCAATGTAATGGACTCGAATGGAACGGAATGGAATGGACAAGAATTGAATTGAATGGACTGGAATGGAATGGAATGGAATGGAATGGAATGCACTCGAACGGATTGGAATGGAATGGACTCGAAA	???????????????????????????????????????????????????????????????????????5????5??????????????????????????????5?????????5???55??'55??5??5????#############	SA:Z:chr21,10698725,-,7S58M86S,0,2;	MC:Z:25M5D126M	RG:Z:HTL2K.6	MQ:i:0	AS:i:104
+HM3G2CCXX160308:2:2107:5883:16006	99	chr1	789493	60	76M5D68M7S	=	789790	448	AATGGAATGTGGTGGGATGGATTCAAATGGAATGGAATGGAATTGAGTGGATTTGAATTGAATGGAATGGAATGGTATGGAATGGAATGGAATGAAATGGACTAGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGGAATGTA	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????##	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:133
+HK3T5CCXX160204:1:2215:26423:37875	145	chr1	789499	39	70M5D48M5I28M	=	224014368	223224720	ATGTGGTGGGGTGGAATCAAATGGAATTGAATGGAATTGAGTCGATTTGAATTGAATGGAATGGAATGGTATGGAATGGAATGGAATGAAATGGACTAGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGGAATGTACTTGAA	#######################?5????5????+55???5?555555+5+5?????+??+55????+5+?5?????55?5?+???????????5???5????????????????&?$?????????????????????????????????	MC:Z:151M	RG:Z:HK3T5.1	MQ:i:60	AS:i:107
+HK35NCCXX160204:2:1115:12073:67937	163	chr1	789502	60	67M5D72M12S	=	789575	224	TGGTGGGATGGATTCAAATGGAATGGAATGGAATTGAGTGGATTTGAATTGAATGGAATGGAATGGTATGGAATGGAATGGAATGAAATGGACTAGAATGGAATGGAATGGACTCGAATGGAATGGAAAGGAATGTACTATGAGAGTAGAG	5++???5????????+????????'????????5????55????5'?5???????????????5??5+?'5???????????????+?+'5?%????+5+55????5????########################################	MC:Z:151M	RG:Z:HK35N.2	MQ:i:60	AS:i:123
+HK3T5CCXX160204:5:1112:23916:44468	147	chr1	789503	60	85M5D41M25S	=	789476	-158	AGTGGGATGGAATGAAATGGAATGGAATGGAATTGAGTGGAATTGAATGGAATGGAATGGAATGGTATGGAATGGAATGGAATGGAATGGACTAGAATGGAATGGAATGGACTCGAATGGCATGGACAGGAGTGGACCCGAATGAAATGGA	################?5??????'+???'+?+???'5??+++5?55?'???????????????5+????????????????5''?????+5???????'?+?????????????????????????????????????????????????	MC:Z:93M5D58M	RG:Z:HK3T5.5	MQ:i:48	AS:i:89
+HM3G2CCXX160308:2:2214:7689:20366	145	chr1	789504	57	65M5D86M	=	224014004	223224346	GTGGGATGGATTCAAATTGACTGGAATGGAATCGTGTGGATTTGAATTGAATGGAATGGAATGGTATGGAATGGAATGGAATGAAATGGACTAGAATGGAATGGAATGGACTCGAATGGAATGGAANGGAATGTACTTGAATTGTATGGAA	####################################??5?+?????5+????5?????????????????????????????????????????????????????????????????????????#????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:31	AS:i:118	CO:Z:needed
+HK3T5CCXX160204:4:1106:25997:53662	163	chr1	789591	18	91S31M5I20M4S	=	789681	226	TAGAATGGAATTGACTCGAACGTAATGGAAATGATTGGACTAGAATGGAATGCAATGAAATGCAATGGAATGAAAGGAGATGGAAGGAAACGAAATGGACTTGAATGGAATGGAATGGACTCAGATAGAATGGAATGCAATGGAATGAATT	??????????????????????????????????????????????????????????????????????????????????????5?+?55???????55???????????????????????5++5?????????##############	MC:Z:11S136M4S	RG:Z:HK3T5.4	MQ:i:41	AS:i:30
+HM3G2CCXX160308:2:2118:19481:39563	83	chr1	789649	20	32M15I104M	=	789482	-303	ATTGGATGGAAAGGAATTGAATGGACTCGAAAGGAAAGGAATGGAATGGAATGGAAAGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGAACTCCAATGGAATGGAATGGACTCGAATAGAATGGAA	#############?5?5????++55+?55???+?5?5+???5????'555?5+???5????+5???5?5??5???5?+???5?5??+5????5????5??????????????5??????????????????????????????????????	MC:Z:103S48M	RG:Z:HM3G2.2	MQ:i:15	AS:i:100
+HK3T5CCXX160204:7:1220:28818:11927	65	chr1	789650	0	131M20S	=	1170	0	TTGTATGGAAGGGAATCAAATGAAATGGAATGGAAGGGAATGAAATGAAATGGAATGGAAGGGAATGAAATAGACTCGAATTGAATGGAATGGAATGAACTCCAATGGAATGGAAAGGACTCGAAAAGAATAGAATAAAATCTGTTGGATT	????????????????????????????????????????????????????????'5???????????????????5???+?????????????????????????????????+5'?55+5??+++??????#################	MC:Z:12S80M59S	RG:Z:HK3T5.7	MQ:i:0	AS:i:55
+HM3G2CCXX160308:2:2205:8998:69361	81	chr1	789650	60	42M5I104M	=	224014451	223224657	TTGTATGGAACGGAATTGAATGGACTCGAAAGGAATGGAATGGAATCGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGAACTCCAATGGAATGGAATGGACTCGAATAGAATGGAATGGAATGGAAA	######??5?5????+?+?????5+?5????5???+5????????+$???????????5????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:56	AS:i:135
+HM3G2CCXX160308:2:1101:18304:53979	99	chr1	789651	40	87M64S	=	789985	427	TGTATGGAACGGAATTGAATGGACTCGAAAGGAATGGAATGGAATGGAATGGAATGGAATGGTATGGAATGGAATGGAATGGAATGGGATCGAATGGGGAGGAATGGACTGAAGTCCACTGGAAAGGAGTGGGCTCGACTAGTGAGGAATG	?????????????5????????????????5?????????????5????????????55???5'5???+5??5????+5???%5???++?+5?+5??######################################################	MC:Z:58S93M	RG:Z:HM3G2.2	MQ:i:58	AS:i:72
+HTL2KCCXX160412:6:2116:13616:52080	177	chr1	789655	0	8S42M5I50M46S	=	10698427	0	GAATTGACTGGAATGGAATTGAATGGACGCGAATGGAATGGAATGTAATGGAAACGAATGGAATGGACTCGAATGGAATGGACTCGAATGGAATGGAATGGAATGGATTCGAACAGAATGGAAAAAATGGAATGGACTTGAATGGAATGGA	############?555??5??????5?5?'5????+????????5?????????????5????????+????????????????5??????????????????????????????????????????????????????????????????	SA:Z:chrUn_KI270442v1,26107,-,85S51M15S,0,4;	MC:Z:110S41M	RG:Z:HTL2K.6	MQ:i:14	AS:i:51
+HK35MCCXX160204:7:2102:18071:59095	163	chr1	789656	60	25M5I121M	=	789957	452	GGAACGGAATTGAATGGACTCGAAAGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGAACTCCAATGGAATGGAATGGACCCGAATAGAATGGAATGGAATGGAAAGGCCTC	?????5?????????????????????????????????????????????????5?????????????+????????5?5????????+??5????????+???????+?????????+?5??5++55+???????##############	MC:Z:151M	RG:Z:HK35M.7	MQ:i:60	AS:i:126
+HK35MCCXX160204:4:1201:25276:57196	99	chr1	789657	40	48M15I88M	=	789815	300	GAACGGAATTGAATGGACTCGAAAGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTGGAATGGAATGGAATGGACTCGAATGGAATGGCATGGACTGGACTCCAATGGAATGGAAAGGAATCGAATAGAATGGAAAGGAATGG	????5?????????+??'5???????????????5?5??5??????????5????5??+???5?5??5+?????55??++??5??????+5??##########################################################	MC:Z:3S142M6S	RG:Z:HK35M.4	MQ:i:60	AS:i:85
+HTL2KCCXX160412:6:2219:30036:29648	99	chr1	789771	60	151M	=	789937	317	CGAATAGAATGGAATGGAATGGAAAGGACTCGAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGATGGAATGGAATGGAATGGACTCGAATGGAATGGAACCGAAAGGAATGGAACGGAACGGAACGGAACGCAATGGAATCGACCC	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????5?????????55??????????????#	MC:Z:151M	RG:Z:HTL2K.6	MQ:i:60	AS:i:151
+HK3T5CCXX160204:5:2101:31649:34693	3169	chr1	789787	9	85S41M25S	=	104013	-6315	AGAGAGGACTGGAATGGAACGGACTCGAAGGGAATGGACTGGAATGGAATGGATTGAACGGAATGGACTGGAGCGGAATGGACTAGAATGGAAAGGAAACGAGTGGGATGGAATGGAGTGGAATGGCGCAAAATGGAGAAGAAAAGGAGGA	????????????????????5??55?+??'????5????5???5??????????55??&5???????&5'??5&$5????????+???5?????????????????'??5?5++'?5?5+?5????#########################	SA:Z:chrUn_KI270438v1,110472,+,5S97M49S,9,3;	MC:Z:5S146M	RG:Z:HK3T5.5	AS:i:31
+HK3T5CCXX160204:4:2120:5132:34254	97	chr1	789788	60	119M32S	=	41875411	0	AATGGAAAGGACTCGAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGATGGAATGGAATGGAATGGACTCGAATGGAATGGAACGGAAAGGAATGGAACGGAACGGAACGGAACGGAAGGGACGCGAACGGAATGGAAGGGAAGGGC	????????????????????????????????+???????????????????5?????????????????????5?????????????5????????5????#################################################	MC:Z:69S82M	RG:Z:HK3T5.4	MQ:i:27	AS:i:114
+HJYFJCCXX160204:4:1214:22313:71401	147	chr1	789789	60	151M	=	789758	-182	ATGGAAAGGACTCGAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGATGGAATGGAATGGAATGGACTCGAATGGAATGGAACCGAAAGGAATGGAACGGAACGGAACGGAACGCAATGGAATCGACCCGAATGGAATGGAATGGAA	???????5+5+?5??5?????????????55???????????5????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HJYFJ.4	MQ:i:60	AS:i:151
+HM3G2CCXX160308:2:1122:4188:47738	163	chr1	789790	60	151M	=	790062	423	TGGAAAGGACTCGAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGGTGGAGTGGAGTGGAGTGGAGTGGAATGGGGTGGAAAGGAGAGAAATGGAACGGAGCGGAAGGGAACGGAATGGAAGCGAACGGAATGGAATGGAATGGAAG	???????????????????5????5+????5??????????????+??????5++????5??5?5????+55?+????#########################################################################	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:60
+HK3T5CCXX160204:1:2217:19015:54401	99	chr1	789802	60	151M	=	790036	385	GAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGATGGAATGGAATGGAATGGACTCGAATGGAATGGAACCGAAAGGAATGGAACGGAACGGAACGGAACGCAATGGAATCGACCCGAATGGAATGGAATGGAATGGAATGGAATGG	?????????????????????????????????????????????????????????????????????????5?5?????????????5?5???????????????????5???????????????????????????????????????	MC:Z:151M	RG:Z:HK3T5.1	MQ:i:60	AS:i:151
+HM3G2CCXX160308:2:1109:22820:24743	2209	chr1	789802	0	67S41M43S	=	85758	0	TGGATTGGAATGGAATGGAATGGGAAGGAATGGAATTGAACAGAGTGGAGCGGAGTGGAGTGGAGTGGAGTGGGATGGAATGGAGTGGAATGGAATCGAATGGGATGGGGAGAGGAAGGGTGAGGGGAGAGTATGGACTGCACGACAGCCG	?????????????????????????????????????????????????????????????????????????+5????55?+?+5???5????+?5?#####################################################	SA:Z:chrUn_KI270442v1,11157,+,5S79M67S,4,5;	MC:Z:16S73M5D21M5D41M	RG:Z:HM3G2.2	AS:i:36
+HM3G2CCXX160308:2:1114:23561:12666	163	chr1	789802	40	73M78S	=	790389	686	GAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATTGACTCGGATGGAATGGAATGGAATGGAGAGCGGAAGAGCGGCGTGGAGGGAAAGAGGGTGAAGTGGAGTGT	?????????????????????????????????????5?????????????????????????????????????????5+5'?+5+55+??55????5??++5????###########################################	MC:Z:52S99M	RG:Z:HM3G2.2	MQ:i:54	AS:i:73	XT:i:107
+HM3G2CCXX160308:2:2203:27417:52959	2145	chr1	789802	0	90S36M25S	=	153291	0	GAGCAGTGTGGATTGGAAGGGAATTGGTTGGAATGGGATGGAACAGAATGTAATGGAGTTGAGTGGAGTGGAGTGGAATGGAATTTAATGGAGTGGGATGGAATGGAGTGGAATGGAGTCGAATGGACTAAAAAGGAATGTAGTGGAATGG	???????????????????????????????????????5??????????55?5?????????5??????????5??????????????5????5?????????5????????5?????+5++55??&5'????????5?55?########	SA:Z:chrY,11293824,-,44S54M53S,0,3;	MC:Z:33S104M14S	RG:Z:HM3G2.2	AS:i:31
+HK35MCCXX160204:2:1217:6411:29015	3219	chr1	789802	0	50S51M50S	=	49601542	-127	GCATGGAAGCCGCGCGTGGGGAAAGGAAGAGGAAGGAAAAGAACCGAAGGGAGTGGGATGGAATGGAGTGGAAGGGAAGGGAATGGGATGGAATGGAATGGTAGGGAAGAGAATGGAATGGAACGAAATGGAATGGAATGGAATGGAATGG	#############################################################################?+??++5?+'5+?5+?+?5+??55+?+???????5???????????5????????????5??????????5???	SA:Z:chr5,49601605,-,87S64M,0,2;chrUn_KN707862v1_decoy,9661,+,50S52M49S,0,4;	MC:Z:127M24S	RG:Z:HK35M.2	AS:i:31
+HK35NCCXX160204:1:1106:7060:45189	2193	chr1	789802	0	26S24M5I49M47S	=	31052792	0	GGGAGAGACCGGAGTGGGAGAGGATAGAGTGGGATGGAATGGAGTGGAATCAAGCAGAGTGGAAAGGTATGGAATGGAATGGAATGGACTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGCAATGGAATGGAATAGAGTG	################################???5+55??55'5+??+?++?'+???55+'555+5+55+5+??????5+??+?555+55????+5+??5???????5??????????????????????????????????????????	SA:Z:chr10,38899886,-,71S80M,0,2;	MC:Z:151M	RG:Z:HK35N.1	AS:i:32
+HK3T5CCXX160204:2:1201:5802:72227	147	chr1	789802	40	75S69M7S	=	789800	-71	ACAGAGGATAGGGGGAACTCGGAGCGCTACGCAGCAAGTGACACGCAATGCCCAGGCATGGGTCGTCCGGTAATGGAGTGGGTTGGAATGGGGTGGAATGGACTTGAATGGGATGGAATGGAATGGAATGGACTTGAATGGAATAGAATGG	#####################################################################################????5''&????????+'++?????????????+'?+?????????+'?????????????????5	MC:Z:71M80S	RG:Z:HK3T5.2	MQ:i:51	AS:i:49
+HM3G2CCXX160308:2:2217:4046:26888	2161	chr1	789802	0	4S30M5I43M69S	=	39775	0	AACAGAGTGGGATGGAATGGAGTGGAATGGAATCACACAGAATTGAATGGAGTGGAATGGAATGGAATGGAATGGAATGGAATGAAATGGAATGGAATGGAATGGAATCAACCCGAGTGAAATTGAATGGAATCGAATGGAATGGAATGGA	##############???5+55555?5?+5+5?+??????55?5?5???5??5??????5?5??5???????????????????????????????????????????????????????????????????????????????????????	SA:Z:chr4,49102543,+,107M44S,0,6;	MC:Z:56S68M5I22M	RG:Z:HM3G2.2	AS:i:32
+HK3T5CCXX160204:1:1219:26798:12297	83	chr1	789804	60	12S139M	=	789541	-402	GGAAGGGCTGGGGTGGGATGGGATGGGGTGGAATGGAATCGAATGGGATGGGATGGAATGGAATGGACTCGAATGGAATGGAACCGAAAGGAATGGAACGGAACGGAACGGAACGCAATGGAATCGACCCGAATGGAATGGAATGGAATGG	############################??5+??5?++?%?++55??55??+?5??+????+????5+5&?+???5+????++?5?+?5??+????+?????++?????????5????5?????5????????????????5?????????	MC:Z:28M5D46M77S	RG:Z:HK3T5.1	MQ:i:40	AS:i:119
+HJYFJCCXX160204:7:2214:23297:36012	2163	chr1	789805	0	16S70M65S	=	49092081	132	AGGGGAAGCCAGGGAATGGGATGGAATGGAGTGGAATGGAATCAAATGGGATAGAATGGATTGTAATGGAATGGAATGGAATGGAATGGAATTGAATGGAATGGAATGGAATGGAATGGAGGGGAATGGAATGGAATGGAATGGAGTGGAA	###############################????55''5??5?5??55'5+?'5???55??5?5?5'?5?5??55???????????????55???????????????????????????5??????????????????????????????	SA:Z:chr4,49092039,+,85M66S,0,3;	MC:Z:61S90M	RG:Z:HJYFJ.7	AS:i:35
+HK35MCCXX160204:5:1108:26707:70328	113	chr1	789805	0	35S20M5I38M53S	=	29568	0	GGGGGTGGAGTGGGGGGGAAGTAAACTGGGTCGCCTGGGATGGGATGGAGTGGAAGGGAGTGGACCGGAATGGGATGGAATGGAATGGAATGGACTCGGCCCGAGTGCAGGGGAATGGAATGGAATGCCATGGAATGGAATCATCCGGAAT	#################################################################################??+?+??55??5+'+%'&555???+5'????????555?5??5?5??+?????+????????????????	SA:Z:chr17,21954755,-,111S31M9S,0,0;chrUn_KN707896v1_decoy,17459,+,24M5D53M74S,0,9;	MC:Z:119S32M	RG:Z:HK35M.5	MQ:i:0	AS:i:32
+HJYFJCCXX160204:7:1201:27194:12490	99	chr1	789942	40	80M5D36M35S	=	790137	342	GAATGGAATGGAATGCAAAGGAATCGAATGGGACAGAATGTATTGGAATGGACTCGAATGGAATGGATAGGAATGGACCCAAATGGAATGGAGTGGAATGGTCTCGAGTGGAATGGAAGGGAATGGAATGGACTCGAAGGGAACGGGATGG	??5?????????????????????????????????????????????????????????????????????5????????5???????55??5??????????????5??555????+5???5????5????555??+??55'5?+55??	MC:Z:5S25M4I74M5D43M	RG:Z:HJYFJ.7	MQ:i:45	AS:i:70
+HM3G2CCXX160308:2:1217:27509:46085	2177	chr1	789942	0	11S52M88S	=	49118886	0	GGAATCATCACGAATGGAATGGAACGCAATAGAATGGGATGGGATGGAATGTATTGGAATGGAAGTTAATCAACACGAATGGAATGGAATGGAAAGGAATGGAAGGAAATGGAATGGAATGGAATGGAATGCAATGAAAAGGAAGGGAAGG	????????????????????????????????????????????????????5????????????5???????5???????????????+??????????????+?+555?????????5?????????????555+?++???########	SA:Z:chr5,49657667,-,20S64M67S,0,3;chrUn_KN707862v1_decoy,4997,-,15S60M76S,0,2;	MC:Z:133M18S	RG:Z:HM3G2.2	AS:i:32
+HK3T5CCXX160204:2:1206:7608:64421	147	chr1	789956	60	151M	=	789752	-355	GCAAGGGAATCGAAGGGGATGGAATGTATTGGAATGGACTCGAATGGCATGGACAGGAGTGGACCCGAATGAAATGGAATGGAATGGAATGGTCTCGAGTGGAATGGGATGGGATGGGATGGGATGCGATGGGATGGGATGGGATGGGATG	########??5???+++?????????++5??'+?55?+?5?????????????5????5????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HK3T5.2	MQ:i:60	AS:i:141
+HK35MCCXX160204:6:2112:25388:7568	2161	chr1	790055	0	33S40M78S	=	49103939	4575	GAGAGGAATGGGATGGGATTTAGTGGGGTGGGATGGAAAGGGATGGGATGGGATGGGATGCGATGGGATGGGAAGGAATGGAACTTAATCAACACGAATGGAACGGAATGCAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGG	################################?5????5?'+?55'??+???5???5+??+'+5?''?5??+??????+??++??????'????5??????+?5???????????????????????????????????????????????	SA:Z:chr4,49099465,+,58M93S,0,1;	MC:Z:50S101M	RG:Z:HK35M.6	AS:i:35
+HTL2KCCXX160412:6:1209:30289:48476	83	chr1	790055	60	28S123M	=	789618	-560	AAGTGGAAGGGGATGAGGGGGTGGCGGTTGGAATGGGATGGGATGGGATGGAATGGAATGGAATGGGATGGGATGGGATGGGATGGGATGGGATTGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATAG	########################################?5??'?5????5??''5?5''555'5'55%5'??+5'55555????5???????55'+55?5??5???5'55????????????'??????5???????????????????	MC:Z:106M45S	RG:Z:HTL2K.6	MQ:i:60	AS:i:78
+HM3G2CCXX160308:2:1209:19654:58919	83	chr1	790056	60	151M	=	790008	-199	GGAAGGGGGTGGGATGGGGTGGGATGGGATGGGATGGGATGGGTTGGGATGGGATGGGATGGGATGGATTGTGATGGGATAGAAGGGAATGGAATGGAATGGAATGGAATGGAATGGAATAGACTCGAAAGGATTGGAATGGAATGGACTC	##############??55'????55?+55??55555??5?5?'+??++5+??5?+?55+?5????????5'++?+??5?5??5?55?55????55+???5'?5??????????????????????5????5????????????????????	MC:Z:111S40M	RG:Z:HM3G2.2	MQ:i:60	AS:i:102
+HM3G2CCXX160308:2:2215:12987:67234	83	chr1	790056	60	5S146M	=	789833	-369	GGAGGGGAATGGGAGGGGATGGGATGGGATGAGAGGGGATGGGAGGGGATGGGATGGGATGGGATGGGATGGATTGGAATGGAATAGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATAGACTCGAAAGGATTGGAATGGAATG	##########??'55??+55???5???55++5??????5++%'55?5555???5???5+????5???????????+?????????????????????????????5?????????????????????????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:121
+HM3G2CCXX160308:2:2101:8968:67234	113	chr1	790066	10	110M6D11M1I29M	=	49104531	0	GGGATGGGATGGGATGGGATGGGAGGGGATGGGAGGGGATGGGATGGGATGGGATGGACTGGAATGGAATGGGATGGAATGGAATGGAATGGTACGGAATGGAATGGAATGGAACGAATGGTAATGGAATGGAATTGAATGGAATGGAATG	###################################5????55+5?5++???55??5?55????5?5555??????555????55??55???5555?????'??????55??5?55?5????????5?????????????????????????	SA:Z:chrUn_KN707896v1_decoy,2751,+,103M48S,0,4;	MC:Z:108S43M	RG:Z:HM3G2.2	MQ:i:0	AS:i:65
+HTL2KCCXX160412:6:2110:6644:12718	99	chr1	790107	60	151M	=	790287	331	GGATGGGATGGGATGGATTTGAATGGAATAGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATAGACTCGAAAGGATTGGAATGGAATGGACTCGAATGGAATGGAATGGACATGAATGGAACGGAATGGAATGGAATGAACTCG	?????????????????????????????????????????????????????????????????????????????????????????????????5??????????????????????????????5????5????5???5????####	MC:Z:151M	RG:Z:HTL2K.6	MQ:i:60	AS:i:151
+HM3G2CCXX160308:2:2123:23815:34729	2225	chr1	790107	0	60M91S	=	49103555	0	GGATAGAATGGGATGGAATGGAAGGGGATAGAATGGAATGGAATGGAATGGAATGGAATGAACCCGTGTGCAATGGAATGGAATGGAATGGAATGGAAGGGATTCAACGCGAATGGAATCAACTCGATTGCAATGGAATGGAATGGAATTG	################################?+????5??5?+???5?????5????5?????+???5?5???????'????+????5????5????+????????5'??????????????????????????????????????????	SA:Z:chr10,41859902,-,31S67M53S,0,2;chrUn_KI270442v1,91567,-,115S36M,0,1;chrUn_JTFH01000872v1_decoy,9,+,41M5I74M5I26M,12,22;	MC:Z:38S104M9S	RG:Z:HM3G2.2	AS:i:33
+HTL2KCCXX160412:5:2208:8400:68605	2129	chr1	790108	0	63M88S	=	41874802	0	GAGGGGATGGGATGGGTTGGTAGGGAATAGAATGGAATGGAATGGAATGGAATGGAATGGAATTTAATGGAATGGAATGGAATGAACCCGTGTGCAATGGAATGGAATGGAATGGAATGGAATGTATTCAACTCGAATGGAATCAACTCGA	########################################????'???5?55+'?5??5?????????5??????5??????????5?+?????5????????????????????????????????????????????????????????	SA:Z:chr4,49137211,+,27S92M32S,0,5;	MC:Z:6S103M42S	RG:Z:HTL2K.5	AS:i:40
+HK35MCCXX160204:7:2119:9019:57548	81	chr1	790137	2	50S52M49S	=	69931	0	GAAGGGGGGGGGTTGTAGGGGAGTGGAATGAAATGGGAGGGAAAGGAAGGGAATGGAAGGGAAGGGAATGGAATGGAATGGAATGGAATAGACTCGAAAGGAAAGGAACCGCATGGAAGCTACTATAATGGAATGGACTGGAATGGAATGG	###############################?5??5+?5??++???55+???????????+?????????????????????????????5???+???????????????5?????????????????????????????????????5??	MC:Z:32M119S	RG:Z:HK35M.7	MQ:i:22	AS:i:42
+HK35NCCXX160204:1:2120:5416:32777	3161	chr1	790137	2	21M5I28M5I33M59S	=	74288	0	GAATGGACTAGAATGGAATGGACATAAATGGAATGAAAAGGAATAGACTGGAAATAAATGAATTGGAATGGAATGGACTCGAATGGAATGGACTAGATTCGAATGGAATGGAAAAGAATGGAATGGATTCGAATGGAATGTGATGGAATGG	###########################?55????5+???5???+??????????????5???5?????5??????????5?????????????????5?????????????????????????????????????????????????????	SA:Z:chrUn_KI270442v1,74288,-,51S100M,60,6;	RG:Z:HK35N.1	AS:i:31
+HM3G2CCXX160308:2:2118:24434:49443	147	chr1	790203	53	151M	=	789932	-422	AATCGAATGGAATGGAAGGGACATGAATGGAACGGAATGGAATGGAATTAACTCTAATGGAATACCATGGAATTTAACGGAATGGAATCCAATGGAATAGACCTGAATGGAATAGAATGGAAGAGACTCGAATGGAATGGAATACAATGGA	#####???555??5+55?5??+?5??????5?&?+55+555?5+5555'??+++'?55?+??55++?'5???+?555&'+?5++5555++5?5+555'555++?5?55???5'????55???+5??5?5??????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:104
+HTL2KCCXX160412:5:2123:31030:28980	2193	chr1	790205	0	60S47M44S	=	56760780	13141	GGAGATGGAATGGAAAGGCACGGACTGCAACCGAAATCGACACACTGGAGCCGAAACTAATCGAATGGGATGGAATGGACATGAATGGAACGGAATGGAATGGAATGGAATGGAATGGAAGGGAATCGAACGGAAGGGAATCGAAGGGAAA	####################################################################################???5+5%+?555''????????''???5???????????????????????????????????????	SA:Z:chrY,56747588,-,98S53M,0,3;	MC:Z:151M	RG:Z:HTL2K.5	AS:i:42
+HK35MCCXX160204:4:1203:32086:55455	163	chr1	790206	40	114M37S	=	790528	473	CGAATGGAATGGAATGGACATGAATGGAACGGAATGGAATGGAATGAACGCGAATGGCATGGAAGGGAATTTAATGGAATGGACTATAATGGAATGGACTGGACTGGAATAGAAGCGAAGAGAAACGGATGGGAGGGAACGGAGGCGAGAG	????????5???????????+??????++55?????????????+'?5&$'$+?+5?'?+''?+'5??++++??5??????'?'???################################################################	MC:Z:151M	RG:Z:HK35M.4	MQ:i:60	AS:i:74
+HJYFJCCXX160204:6:1109:5873:34166	65	chr1	790207	0	30S97M24S	=	10693901	0	TAATGGAATGAAATTTACTCAAATGGAGTGGAATGGAATGGAATGGACATGAATGGAACAGAATGGAATGGAATGTTCTCGAATGGAACACAAAGGAATTTAATGGAATGGACTCTAATGGAATGGAAGGGAATGGAATGGAATGAACTTG	????????????????????????????5????????????????????5?????????????????????????????'5??????????????????????55+????????'?????5???????+?+?????????????+??####	SA:Z:chr10,38487562,+,116S31M4S,0,0;	MC:Z:33S99M19S	RG:Z:HJYFJ.6	MQ:i:7	AS:i:72
+HK35MCCXX160204:3:2217:25611:48529	163	chr1	790257	33	151M	=	790402	296	GAATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGACTTGAATGGAATAGAATGGAAGAGACTCGAATGGAATGGAATGCAATGGAATGGAATGGAATGGAATGTAATGGAATGGACTGGAGTGGAATAGAATGGAAGGG	???????????????????????????????????????????????????????????????????5????5??5??5????????5++5??????+?5'?+++??+5???#######################################	MC:Z:151M	RG:Z:HK35M.3	MQ:i:60	AS:i:114
+HM3G2CCXX160308:2:1222:14418:40425	147	chr1	790332	60	151M	=	790243	-240	GAATGGAATGGAATACAATGGAATTTAATGGAATGGACTCTAATGGAATGGACTTGAATGGAATAGAATGGAAGAGACTCGAATGGAATGGAATGCAATGGAATGGACTCGAATGGAATGGAATGGAATTGACTCAGATGGAATGGAATGG	????????????5??????5???5???5?????5?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????	MC:Z:151M	RG:Z:HM3G2.2	MQ:i:60	AS:i:151	CO:Z:needed
+HTL2KCCXX160412:5:1214:2920:10240	99	chr1	790408	27	63M5I73M10S	=	790478	221	ACTCTAATGGAATGGAATGCAAGGGACTGGACTCAAATGGAATGGAATGGAATTGACTCAAATGGTAGGGAAAGGAATTGAATGGACTCGAAAGGATTGGGATGGAGTACAGGGGAATGGACTCGAATGGAATGGAATGGACGGAACTCGA	+?55??????????????????????&5????????5????????????????????????????5?+??????????????5??????????????????????????5??5???5???????????????+????5???##########	MC:Z:151M	RG:Z:HTL2K.5	MQ:i:27	AS:i:65	CO:Z:needed
+HTL2KCCXX160412:5:1214:2920:10240	147	chr1	790478	27	151M	=	790408	-221	AATTGAATAGAATCGAAAGGAATGGGATGGAGTACAGTGGAATGAACTCGAATAGAATGGAAAGGAATGAACTCGAATGCAATGTTATGCAATGGAATGGACCCAAATGGAATGGAATGTAATTGACTCGAATGGAATTGAATGGAATGGA	################################????5?+??55'55???????5????''??5??????????&???????????????5??????????????????????????????????????+??????????????????????	MC:Z:63M5I73M10S	RG:Z:HTL2K.5	MQ:i:27	AS:i:59
diff -Nru htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/tribble/gff/canonical_gene.gff3 htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/gff/canonical_gene.gff3
--- htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/tribble/gff/canonical_gene.gff3	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/gff/canonical_gene.gff3	2020-07-08 16:28:01.000000000 +0000
@@ -1,8 +1,8 @@
 ##gff-version 3.2.1
 ##sequence-region ctg123 1 1497228
-ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
-ctg123	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs00001;Parent=gene00001
-ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001;Name=EDEN.1
+ctg123	.	gene	1000	9000	1.03e03	+	.	ID=gene00001;Name=EDEN
+ctg123	.	TF_binding_site	1000	1012	0.999	+	.	ID=tfbs00001;Parent=gene00001
+ctg123	.	mRNA	1050	9000	1.37	+	.	ID=mRNA00001;Parent=gene00001;Name=EDEN.1
 ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001;Name=EDEN.2
 ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001;Name=EDEN.3
 ctg123	.	exon	1300	1500	.	+	.	ID=exon00001;Parent=mRNA00003
diff -Nru htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/tribble/gff/feature_extends_past_circular_region.gff3 htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/gff/feature_extends_past_circular_region.gff3
--- htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/tribble/gff/feature_extends_past_circular_region.gff3	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/gff/feature_extends_past_circular_region.gff3	2020-07-08 16:28:01.000000000 +0000
@@ -1,4 +1,4 @@
 ##gff-version 3
 ##sequence-region   1 1 10
 1	.	region	1	10	.	.	.	ID=chromosome:1; Is_circular=true
-1	.	biological_region	7	11	.	.	.	
\ No newline at end of file
+1	.	biological_region	7	11	.	.	.	.
\ No newline at end of file
diff -Nru htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/tribble/gff/url_encoding.gff3 htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/gff/url_encoding.gff3
--- htsjdk-2.22.0+dfsg/src/test/resources/htsjdk/tribble/gff/url_encoding.gff3	2020-05-21 22:48:09.000000000 +0000
+++ htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/tribble/gff/url_encoding.gff3	2020-07-08 16:28:01.000000000 +0000
@@ -1,3 +1,3 @@
 ##gff-version 3
 ##sequence-region   1 1 10
-the%20contig	a%20source%20%26%20also%20a%20str*)%25nge%20source	a%20region	1	10	.	.	.	ID=this%20is%20the%20ID%20of%20this%20wacky%20feature%5E%26%25%23%23%24%25*%26%3E%2C.%20%2C.; Another%20key=Another%3Dvalue
\ No newline at end of file
+the contig	a source %26 also a str*)%25nge source	a region	1	10	.	.	.	ID=this is the ID of this wacky feature%5E%26%25%23%23%24%25*%26%3E%2C. %2C.; Another key=Another%3Dvalue,And a second%2C value
\ No newline at end of file