diff -Nru mitcr-1.0.2/.flow mitcr-1.0.3/.flow
--- mitcr-1.0.2/.flow	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/.flow	1970-01-01 00:00:00.000000000 +0000
@@ -1,8 +0,0 @@
-[branchname]
-master = default
-develop = develop
-feature = feature/
-release = release/
-hotfix = hotfix/
-support = support/
-
diff -Nru mitcr-1.0.2/.hg_archival.txt mitcr-1.0.3/.hg_archival.txt
--- mitcr-1.0.2/.hg_archival.txt	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/.hg_archival.txt	1970-01-01 00:00:00.000000000 +0000
@@ -1,4 +0,0 @@
-repo: 844e945cd218ff60d9c7f5a006248ec49aa58a16
-node: 4018053dcaa1bb3bf00f79f85beef3778a3f0004
-branch: default
-tag: v1.0.2
diff -Nru mitcr-1.0.2/.hgignore mitcr-1.0.3/.hgignore
--- mitcr-1.0.2/.hgignore	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/.hgignore	1970-01-01 00:00:00.000000000 +0000
@@ -1,8 +0,0 @@
-target/
-nbactions.*\.xml$
-nb-configuration.xml$
-\.log$
-\.log\.
-\.iml$
-.idea\/
-\.DS_Store$
diff -Nru mitcr-1.0.2/.hgtags mitcr-1.0.3/.hgtags
--- mitcr-1.0.2/.hgtags	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/.hgtags	1970-01-01 00:00:00.000000000 +0000
@@ -1,3 +0,0 @@
-a4c341c82927419185658d70ad2ebb2722b067c4 v1.0
-be7bfb9355909c516c0924b9e44fb32c7ff33276 d_segment_rc
-cb429a954d695e15200132061c4757d035defe6c v1.0.1
diff -Nru mitcr-1.0.2/debian/changelog mitcr-1.0.3/debian/changelog
--- mitcr-1.0.2/debian/changelog	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/changelog	2013-10-10 20:27:44.000000000 +0000
@@ -1,3 +1,9 @@
+mitcr (1.0.3-1~saucy) saucy; urgency=low
+
+  * Release 1.0.3
+
+ -- Dmitriy Bolotin <bolotin.dmitriy@gmail.com>  Thu, 10 Oct 2013 19:15:56 +0400
+
 mitcr (1.0.2-10~saucy) saucy; urgency=low
 
   * Corrections to start script
diff -Nru mitcr-1.0.2/debian/control mitcr-1.0.3/debian/control
--- mitcr-1.0.2/debian/control	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/control	2013-10-10 20:27:44.000000000 +0000
@@ -4,7 +4,7 @@
 Maintainer: Dmitriy Bolotin <bolotin.dmitriy@gmail.com>
 Uploaders: Dmitriy Bolotin <bolotin.dmitriy@gmail.com>
 Build-Depends: debhelper (>= 7), cdbs, openjdk-7-jdk, maven-debian-helper (>= 1.5)
-Build-Depends-Indep: libcommons-cli-java, libmicommons-java, libtrove3-java (>= 3.0.3),  
+Build-Depends-Indep: libcommons-cli-java, libmicommons-java (>= 1.0.3), libtrove3-java (>= 3.0.3),  
  junit4, openjdk-7-doc, libmaven-javadoc-plugin-java 
 Standards-Version: 3.9.2
 Vcs-Svn: svn://svn.debian.org/svn/pkg-java/trunk/mitcr
diff -Nru mitcr-1.0.2/debian/maven.properties mitcr-1.0.3/debian/maven.properties
--- mitcr-1.0.2/debian/maven.properties	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/maven.properties	2013-10-10 20:27:44.000000000 +0000
@@ -2,7 +2,7 @@
 # For example:
 # maven.test.skip=true
 
-timestamp=15-08-2013 13:39 +0400
+timestamp=09-10-2013 10:05 +0200
 hgBranch=default
-changeSetDate=2013-08-12 15:19 +0400
-changeSet=4018053dcaa1
+changeSetDate=2013-10-09 10:03 +0200
+changeSet=21d90ccd8c0d
diff -Nru mitcr-1.0.2/debian/patches/01_pom_cleanup.patch mitcr-1.0.3/debian/patches/01_pom_cleanup.patch
--- mitcr-1.0.2/debian/patches/01_pom_cleanup.patch	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/patches/01_pom_cleanup.patch	1970-01-01 00:00:00.000000000 +0000
@@ -1,237 +0,0 @@
-Description: pom cleanup
- TODO: Put a short summary on the line above and replace this paragraph
- with a longer explanation of this change. Complete the meta-information
- with other relevant fields (see below for details). To make it easier, the
- information below has been extracted from the changelog. Adjust it or drop
- it.
- .
- mitcr (1.0.2-1) UNRELEASED; urgency=low
- .
-   * Initial release (Closes: #nnnn)  <nnnn is the bug number of your
-     ITP>
-Author: Dmitriy Bolotin <bolotin.dmitriy@gmail.com>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- mitcr-1.0.2.orig/pom.xml
-+++ mitcr-1.0.2/pom.xml
-@@ -28,12 +28,6 @@
-     <packaging>jar</packaging>
-     <name>MiTCR</name>
- 
--    <parent>
--        <groupId>org.sonatype.oss</groupId>
--        <artifactId>oss-parent</artifactId>
--        <version>7</version>
--    </parent>
--
-     <description>
-         MiTCR is an open source software package aimed at extraction of information
-         on repertoire of T-cell clones from Next Generation Sequencing (NGS) data.
-@@ -107,7 +101,6 @@
- 
-     <properties>
-         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
--        <maven.build.timestamp.format>yyyy-MM-dd HH:mm Z</maven.build.timestamp.format>
-     </properties>
- 
-     <scm>
-@@ -116,116 +109,9 @@
-         <url>https://bitbucket.org/milaboratory/mitcr/src/?at=v1.0.2</url>
-     </scm>
- 
--    <profiles>
--        <profile>
--            <id>vcs.info</id>
--
--            <activation>
--                <!--<property>-->
--                <!--<name>vcsinfo</name>-->
--                <!--</property>-->
--                <file>
--                    <exists>${basedir}/.hg</exists>
--                </file>
--            </activation>
--
--            <build>
--                <plugins>
--                    <plugin>
--                        <artifactId>maven-antrun-plugin</artifactId>
--                        <version>1.7</version>
--                        <executions>
--                            <execution>
--                                <phase>validate</phase>
--                                <configuration>
--                                    <target>
--                                        <loadfile srcFile="./.hg/branch" property="hgBranch"/>
--                                    </target>
--                                    <exportAntProperties>true</exportAntProperties>
--                                </configuration>
--                                <goals>
--                                    <goal>run</goal>
--                                </goals>
--                            </execution>
--                        </executions>
--                    </plugin>
--
--                    <!-- <plugin>
--                        <groupId>org.codehaus.mojo</groupId>
--                        <artifactId>buildnumber-maven-plugin</artifactId>
--                        <version>1.1</version>
--                        <executions>
--                            <execution>
--                                <phase>validate</phase>
--                                <goals>
--                                    <goal>hgchangeset</goal>
--                                </goals>
--                            </execution>
--                        </executions>
--                    </plugin> -->
--                </plugins>
--            </build>
--        </profile>
--
--        <profile>
--            <id>no.vcs.info</id>
--
--            <activation>
--                <!--<property>-->
--                <!--<name>!vcsinfo</name>-->
--                <!--</property>-->
--                <file>
--                    <missing>${basedir}/.hg</missing>
--                </file>
--            </activation>
--
--            <build>
--                <plugins>
--                    <plugin>
--                        <artifactId>maven-antrun-plugin</artifactId>
--                        <version>1.7</version>
--                        <executions>
--                            <execution>
--                                <phase>validate</phase>
--                                <configuration>
--                                    <target>
--                                        <property name="hgBranch" value="unknown"/>
--                                        <property name="changeSet" value="unknown"/>
--                                        <property name="changeSetDate" value="unknown"/>
--                                    </target>
--                                    <exportAntProperties>true</exportAntProperties>
--                                </configuration>
--                                <goals>
--                                    <goal>run</goal>
--                                </goals>
--                            </execution>
--                        </executions>
--                    </plugin>
--                </plugins>
--            </build>
--        </profile>
--    </profiles>
--
-     <build>
-         <plugins>
-             <plugin>
--                <groupId>com.keyboardsamurais.maven</groupId>
--                <artifactId>maven-timestamp-plugin</artifactId>
--                <version>1.0</version>
--                <configuration>
--                    <propertyName>timestamp</propertyName>
--                    <timestampPattern>dd-MM-yyyy HH:mm Z</timestampPattern>
--                </configuration>
--                <executions>
--                    <execution>
--                        <goals>
--                            <goal>create</goal>
--                        </goals>
--                    </execution>
--                </executions>
--            </plugin>
--
--            <plugin>
-                 <groupId>org.apache.maven.plugins</groupId>
-                 <artifactId>maven-jar-plugin</artifactId>
-                 <version>2.3.1</version>
-@@ -245,70 +131,6 @@
-             </plugin>
- 
-             <plugin>
--                <groupId>org.apache.maven.plugins</groupId>
--                <artifactId>maven-shade-plugin</artifactId>
--                <version>2.0</version>
--                <executions>
--                    <execution>
--                        <phase>package</phase>
--                        <goals>
--                            <goal>shade</goal>
--                        </goals>
--                        <configuration>
--                            <createDependencyReducedPom>false</createDependencyReducedPom>
--                            <minimizeJar>true</minimizeJar>
--                            <filters>
--                                <filter>
--                                    <artifact>org.jdom:jdom</artifact>
--                                    <includes>
--                                        <include>**</include>
--                                    </includes>
--                                </filter>
--                                <filter>
--                                    <artifact>*:*</artifact>
--                                    <excludes>
--                                        <exclude>META-INF/localization/*</exclude>
--                                        <exclude>META-INF/*.txt</exclude>
--                                        <exclude>META-INF/*.xml</exclude>
--                                        <exclude>JDOMAbout*.class</exclude>
--                                    </excludes>
--                                </filter>
--                            </filters>
--                            <!-- <outputFile>target/mitcr.jar</outputFile> -->
--                            <transformers>
--                                <transformer
--                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
--                                    <mainClass>com.milaboratory.mitcr.cli.Main</mainClass>
--                                </transformer>
--                                <transformer
--                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
--                                    <resource>META-INF/README</resource>
--                                    <file>README.txt</file>
--                                </transformer>
--                                <transformer
--                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
--                                    <resource>META-INF/LICENSE</resource>
--                                    <file>LICENSE.txt</file>
--                                </transformer>
--                                <transformer
--                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
--                                    <resource>META-INF/AUTHORS</resource>
--                                    <file>AUTHORS.txt</file>
--                                </transformer>
--                                <transformer
--                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
--                                    <resource>META-INF/NOTICE</resource>
--                                    <file>NOTICE.txt</file>
--                                </transformer>
--                            </transformers>
--                            <shadedArtifactAttached>true</shadedArtifactAttached>
--                            <shadedClassifierName>distribution</shadedClassifierName>
--                        </configuration>
--                    </execution>
--                </executions>
--            </plugin>
--
--            <plugin>
-                 <groupId>org.apache.maven.plugins</groupId>
-                 <artifactId>maven-resources-plugin</artifactId>
-                 <version>2.4.3</version>
diff -Nru mitcr-1.0.2/debian/patches/02_test_ignore.patch mitcr-1.0.3/debian/patches/02_test_ignore.patch
--- mitcr-1.0.2/debian/patches/02_test_ignore.patch	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/patches/02_test_ignore.patch	1970-01-01 00:00:00.000000000 +0000
@@ -1,43 +0,0 @@
-Description: <short summary of the patch>
- TODO: Put a short summary on the line above and replace this paragraph
- with a longer explanation of this change. Complete the meta-information
- with other relevant fields (see below for details). To make it easier, the
- information below has been extracted from the changelog. Adjust it or drop
- it.
- .
- mitcr (1.0.2-2~precise) precise; urgency=low
- .
-   * Initial release
-Author: Dmitriy Bolotin <bolotin.dmitriy@gmail.com>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- mitcr-1.0.2.orig/src/test/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculatorTest.java
-+++ mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculatorTest.java
-@@ -3,6 +3,7 @@ package com.milaboratory.mitcr.clonegene
- import org.apache.commons.math.random.*;
- import org.apache.commons.math.stat.descriptive.SummaryStatistics;
- import org.junit.Assert;
-+import org.junit.Ignore;
- import org.junit.Test;
- 
- public class AverageQualityCalculatorTest {
-@@ -25,6 +26,7 @@ public class AverageQualityCalculatorTes
-         Assert.assertEquals(0.5, ss.getStandardDeviation(), 0.05);
-     }
- 
-+    @Ignore
-     @Test
-     public void test2() throws Exception {
-         RandomGenerator rg = new Well19937a();
diff -Nru mitcr-1.0.2/debian/patches/03_su_script.patch mitcr-1.0.3/debian/patches/03_su_script.patch
--- mitcr-1.0.2/debian/patches/03_su_script.patch	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/patches/03_su_script.patch	1970-01-01 00:00:00.000000000 +0000
@@ -1,92 +0,0 @@
-Description: <short summary of the patch>
- TODO: Put a short summary on the line above and replace this paragraph
- with a longer explanation of this change. Complete the meta-information
- with other relevant fields (see below for details). To make it easier, the
- information below has been extracted from the changelog. Adjust it or drop
- it.
- .
- mitcr (1.0.2-9~SERIES) SERIES; urgency=low
- .
-   * Free memory calculation algorithm fixed
-Author: Dmitriy Bolotin <bolotin.dmitriy@gmail.com>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- /dev/null
-+++ mitcr-1.0.2/src/scripts/mitcr
-@@ -0,0 +1,49 @@
-+#!/bin/bash
-+
-+freem=`free -m | sed 's/\s\+/ /g' | cut -d' ' -f4 | head -n 2 | tail -n 1 | tr -d '\n'`
-+buffersm=`free -m | sed 's/\s\+/ /g' | cut -d' ' -f6 | head -n 2 | tail -n 1 | tr -d '\n'`
-+cachedm=`free -m | sed 's/\s\+/ /g' | cut -d' ' -f7 | head -n 2 | tail -n 1 | tr -d '\n'`
-+
-+free_memory=`echo "$freem+$buffersm+$cachedm" | bc`
-+
-+java_memory=`echo "$free_memory*9/10" | bc`
-+
-+classpath="/usr/share/java/micommons.jar:/usr/share/java/redberry-pipe.jar:/usr/share/java/jdom1.jar:/usr/share/java/commons-compress.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-cli.jar:/usr/share/java/trove3.jar:/usr/share/java/mitcr.jar"
-+xmx="${java_memory}m"
-+params=("$@")
-+
-+java_path=`ls -1 /usr/lib/jvm | grep java-7-openjdk | grep -v common | tr -d '\n'`
-+if [ -z "$java_path" ]; then
-+    java_path=`ls -1 /usr/lib/jvm | grep java-7 | head -n 1 | tr -d '\n'`
-+fi
-+java_path="/usr/lib/jvm/${java_path}/bin/java"
-+
-+if [ ! -f "$java_path" ]; then
-+    echo "Can't find Java 7 on your system."
-+fi
-+
-+auto_memory=true
-+
-+for ((n=0; n < ${#params[@]}; n++))
-+do
-+    if [[ "${params[$n]}" == -Xmx* ]]
-+    then
-+	xmx="${params[$n]:4}"
-+	unset params[$n]
-+	auto_memory=false
-+    fi
-+done
-+
-+if $auto_memory ; then
-+    echo "Max java heap space automatically set to ${xmx} (90% of free memory). Use '-Xmx' option to adjust this value."
-+else
-+    echo "Java heap space set to ${xmx}."
-+fi
-+
-+options="-XX:+AggressiveOpts"
-+
-+if [[ `uname -i` == "x86_64" ]]; then
-+    options="$options -XX:+DoEscapeAnalysis"
-+fi
-+
-+eval "${java_path} -Dexecutable=mitcr $options -cp $classpath -Xmx${xmx} com.milaboratory.mitcr.cli.Main ${params[@]}"
---- mitcr-1.0.2.orig/src/main/java/com/milaboratory/mitcr/cli/Main.java
-+++ mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/Main.java
-@@ -439,9 +439,9 @@ public class Main {
-             }
-         });
-         final String executable = System.getProperty("executable", "java -jar mitcr.jar");
--        err.println("usage: " + executable + " -preset <preset name> [options] input_file output_file.cls");
--        err.println("       " + executable + " -preset <preset name> [options] input_file output_file.txt");
--        err.println("       " + executable + " -preset <preset name> [options] -export newPresetName");
-+        err.println("usage: " + executable + " -pset <preset name> [options] input_file output_file.cls");
-+        err.println("       " + executable + " -pset <preset name> [options] input_file output_file.txt");
-+        err.println("       " + executable + " -pset <preset name> [options] -export newPresetName");
-         err.println();
- 
-         formatter.printOptions(new PrintWriter(err, true), 85, options, 2, 3);
diff -Nru mitcr-1.0.2/debian/patches/pom_cleanup.patch mitcr-1.0.3/debian/patches/pom_cleanup.patch
--- mitcr-1.0.2/debian/patches/pom_cleanup.patch	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/debian/patches/pom_cleanup.patch	2013-10-10 20:27:44.000000000 +0000
@@ -0,0 +1,237 @@
+Description: <short summary of the patch>
+ TODO: Put a short summary on the line above and replace this paragraph
+ with a longer explanation of this change. Complete the meta-information
+ with other relevant fields (see below for details). To make it easier, the
+ information below has been extracted from the changelog. Adjust it or drop
+ it.
+ .
+ mitcr (1.0.3-1~SERIES) SERIES; urgency=low
+ .
+   * Release 1.0.3
+Author: Dmitriy Bolotin <bolotin.dmitriy@gmail.com>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- mitcr-1.0.3.orig/pom.xml
++++ mitcr-1.0.3/pom.xml
+@@ -29,12 +29,6 @@
+     <name>MiTCR</name>
+     <url>http://mitcr.milaboratory.com/</url>
+ 
+-    <parent>
+-        <groupId>org.sonatype.oss</groupId>
+-        <artifactId>oss-parent</artifactId>
+-        <version>7</version>
+-    </parent>
+-
+     <description>
+         MiTCR is an open source software package aimed at extraction of information
+         on repertoire of T-cell clones from Next Generation Sequencing (NGS) data.
+@@ -122,119 +116,9 @@
+         <url>http://dev.milaboratory.com/</url>
+     </issueManagement>
+ 
+-    <profiles>
+-        <profile>
+-            <id>vcs.info</id>
+-
+-            <activation>
+-                <!--<property>-->
+-                <!--<name>vcsinfo</name>-->
+-                <!--</property>-->
+-                <file>
+-                    <exists>${basedir}/../.hg</exists>
+-                </file>
+-            </activation>
+-
+-            <build>
+-                <plugins>
+-                    <plugin>
+-                        <artifactId>maven-antrun-plugin</artifactId>
+-                        <version>1.7</version>
+-                        <executions>
+-                            <execution>
+-                                <phase>validate</phase>
+-                                <configuration>
+-                                    <target>
+-                                        <loadfile srcFile="../.hg/branch" property="hgBranch"/>
+-                                    </target>
+-                                    <exportAntProperties>true</exportAntProperties>
+-                                </configuration>
+-                                <goals>
+-                                    <goal>run</goal>
+-                                </goals>
+-                            </execution>
+-                        </executions>
+-                    </plugin>
+-
+-                    <plugin>
+-                        <groupId>org.codehaus.mojo</groupId>
+-                        <artifactId>buildnumber-maven-plugin</artifactId>
+-                        <version>1.1</version>
+-                        <executions>
+-                            <execution>
+-                                <phase>validate</phase>
+-                                <goals>
+-                                    <goal>hgchangeset</goal>
+-                                </goals>
+-                            </execution>
+-                        </executions>
+-                        <configuration>
+-                            <scmDirectory>./..</scmDirectory>
+-                        </configuration>
+-                    </plugin>
+-                </plugins>
+-            </build>
+-        </profile>
+-
+-        <profile>
+-            <id>no.vcs.info</id>
+-
+-            <activation>
+-                <!--<property>-->
+-                <!--<name>!vcsinfo</name>-->
+-                <!--</property>-->
+-                <file>
+-                    <missing>${basedir}/../.hg</missing>
+-                </file>
+-            </activation>
+-
+-            <build>
+-                <plugins>
+-                    <plugin>
+-                        <artifactId>maven-antrun-plugin</artifactId>
+-                        <version>1.7</version>
+-                        <executions>
+-                            <execution>
+-                                <phase>validate</phase>
+-                                <configuration>
+-                                    <target>
+-                                        <property name="hgBranch" value="unknown"/>
+-                                        <property name="changeSet" value="unknown"/>
+-                                        <property name="changeSetDate" value="unknown"/>
+-                                    </target>
+-                                    <exportAntProperties>true</exportAntProperties>
+-                                </configuration>
+-                                <goals>
+-                                    <goal>run</goal>
+-                                </goals>
+-                            </execution>
+-                        </executions>
+-                    </plugin>
+-                </plugins>
+-            </build>
+-        </profile>
+-    </profiles>
+-
+     <build>
+         <plugins>
+             <plugin>
+-                <groupId>com.keyboardsamurais.maven</groupId>
+-                <artifactId>maven-timestamp-plugin</artifactId>
+-                <version>1.0</version>
+-                <configuration>
+-                    <propertyName>timestamp</propertyName>
+-                    <timestampPattern>dd-MM-yyyy HH:mm Z</timestampPattern>
+-                </configuration>
+-                <executions>
+-                    <execution>
+-                        <goals>
+-                            <goal>create</goal>
+-                        </goals>
+-                    </execution>
+-                </executions>
+-            </plugin>
+-
+-            <plugin>
+                 <groupId>org.apache.maven.plugins</groupId>
+                 <artifactId>maven-jar-plugin</artifactId>
+                 <version>2.3.1</version>
+@@ -254,76 +138,6 @@
+             </plugin>
+ 
+             <plugin>
+-                <groupId>org.apache.maven.plugins</groupId>
+-                <artifactId>maven-shade-plugin</artifactId>
+-                <version>2.0</version>
+-                <executions>
+-                    <execution>
+-                        <phase>package</phase>
+-                        <goals>
+-                            <goal>shade</goal>
+-                        </goals>
+-                        <configuration>
+-                            <createDependencyReducedPom>false</createDependencyReducedPom>
+-                            <minimizeJar>true</minimizeJar>
+-                            <filters>
+-                                <filter>
+-                                    <artifact>org.jdom:jdom</artifact>
+-                                    <includes>
+-                                        <include>**</include>
+-                                    </includes>
+-                                </filter>
+-                                <filter>
+-                                    <artifact>com.milaboratory:micommons</artifact>
+-                                    <includes>
+-                                        <include>**</include>
+-                                    </includes>
+-                                </filter>
+-                                <filter>
+-                                    <artifact>*:*</artifact>
+-                                    <excludes>
+-                                        <exclude>META-INF/localization/*</exclude>
+-                                        <exclude>META-INF/*.txt</exclude>
+-                                        <exclude>META-INF/*.xml</exclude>
+-                                        <exclude>JDOMAbout*.class</exclude>
+-                                    </excludes>
+-                                </filter>
+-                            </filters>
+-                            <!-- <outputFile>target/mitcr.jar</outputFile> -->
+-                            <transformers>
+-                                <transformer
+-                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+-                                    <mainClass>com.milaboratory.mitcr.cli.Main</mainClass>
+-                                </transformer>
+-                                <transformer
+-                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
+-                                    <resource>META-INF/README</resource>
+-                                    <file>README.txt</file>
+-                                </transformer>
+-                                <transformer
+-                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
+-                                    <resource>META-INF/LICENSE</resource>
+-                                    <file>LICENSE.txt</file>
+-                                </transformer>
+-                                <transformer
+-                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
+-                                    <resource>META-INF/AUTHORS</resource>
+-                                    <file>AUTHORS.txt</file>
+-                                </transformer>
+-                                <transformer
+-                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
+-                                    <resource>META-INF/NOTICE</resource>
+-                                    <file>NOTICE.txt</file>
+-                                </transformer>
+-                            </transformers>
+-                            <shadedArtifactAttached>true</shadedArtifactAttached>
+-                            <shadedClassifierName>distribution</shadedClassifierName>
+-                        </configuration>
+-                    </execution>
+-                </executions>
+-            </plugin>
+-
+-            <plugin>
+                 <groupId>org.apache.maven.plugins</groupId>
+                 <artifactId>maven-resources-plugin</artifactId>
+                 <version>2.4.3</version>
diff -Nru mitcr-1.0.2/debian/patches/series mitcr-1.0.3/debian/patches/series
--- mitcr-1.0.2/debian/patches/series	2013-09-17 14:52:58.000000000 +0000
+++ mitcr-1.0.3/debian/patches/series	2013-10-10 20:27:44.000000000 +0000
@@ -1,3 +1 @@
-01_pom_cleanup.patch
-02_test_ignore.patch
-03_su_script.patch
+pom_cleanup.patch
diff -Nru mitcr-1.0.2/l4j.xml mitcr-1.0.3/l4j.xml
--- mitcr-1.0.2/l4j.xml	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/l4j.xml	1970-01-01 00:00:00.000000000 +0000
@@ -1,43 +0,0 @@
-<!--
-  ~ MiTCR <http://milaboratory.com>
-  ~
-  ~ Copyright (c) 2010-2013:
-  ~     Bolotin Dmitriy     <bolotin.dmitriy@gmail.com>
-  ~     Chudakov Dmitriy    <chudakovdm@mail.ru>
-  ~
-  ~ MiTCR is free software: you can redistribute it and/or modify it
-  ~ under the terms of the GNU General Public License as published by the Free
-  ~ Software Foundation, either version 3 of the License, or (at your option)
-  ~ any later version.
-  ~
-  ~ This program is distributed in the hope that it will be useful, but WITHOUT
-  ~ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-  ~ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
-  ~ more details.
-  ~
-  ~ You should have received a copy of the GNU General Public License along
-  ~ with this program. If not, see <http://www.gnu.org/licenses/>.
-  -->
-<launch4jConfig>
-    <dontWrapJar>false</dontWrapJar>
-    <headerType>console</headerType>
-    <jar>/Volumes/Data/Projects/MiLaboratory/mitcr/target/mitcr.jar</jar>
-    <outfile>/Volumes/Data/Projects/MiLaboratory/mitcr/target/mitcr.exe</outfile>
-    <errTitle></errTitle>
-    <cmdLine></cmdLine>
-    <chdir></chdir>
-    <priority>normal</priority>
-    <downloadUrl>http://java.com/download</downloadUrl>
-    <supportUrl></supportUrl>
-    <customProcName>false</customProcName>
-    <stayAlive>false</stayAlive>
-    <manifest></manifest>
-    <icon></icon>
-    <jre>
-        <path></path>
-        <minVersion>1.7.0</minVersion>
-        <maxVersion></maxVersion>
-        <jdkPreference>preferJre</jdkPreference>
-        <maxHeapPercent>70</maxHeapPercent>
-    </jre>
-</launch4jConfig>
\ No newline at end of file
diff -Nru mitcr-1.0.2/pom.xml mitcr-1.0.3/pom.xml
--- mitcr-1.0.2/pom.xml	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/pom.xml	2013-10-09 08:03:10.000000000 +0000
@@ -24,9 +24,10 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mitcr</artifactId>
-    <version>1.0.2</version>
+    <version>1.0.3</version>
     <packaging>jar</packaging>
     <name>MiTCR</name>
+    <url>http://mitcr.milaboratory.com/</url>
 
     <parent>
         <groupId>org.sonatype.oss</groupId>
@@ -85,7 +86,7 @@
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>micommons</artifactId>
-            <version>0.9</version>
+            <version>1.0.3</version>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>
@@ -112,10 +113,15 @@
 
     <scm>
         <connection>scm:hg:http://bitbucket.org/milaboratory/mitcr</connection>
-        <tag>v1.0.2</tag>
-        <url>https://bitbucket.org/milaboratory/mitcr/src/?at=v1.0.2</url>
+        <tag>v1.0.3</tag>
+        <url>https://bitbucket.org/milaboratory/mitcr/src/?at=v1.0.3</url>
     </scm>
 
+    <issueManagement>
+        <system>YouTrack</system>
+        <url>http://dev.milaboratory.com/</url>
+    </issueManagement>
+
     <profiles>
         <profile>
             <id>vcs.info</id>
@@ -125,7 +131,7 @@
                 <!--<name>vcsinfo</name>-->
                 <!--</property>-->
                 <file>
-                    <exists>${basedir}/.hg</exists>
+                    <exists>${basedir}/../.hg</exists>
                 </file>
             </activation>
 
@@ -139,7 +145,7 @@
                                 <phase>validate</phase>
                                 <configuration>
                                     <target>
-                                        <loadfile srcFile="./.hg/branch" property="hgBranch"/>
+                                        <loadfile srcFile="../.hg/branch" property="hgBranch"/>
                                     </target>
                                     <exportAntProperties>true</exportAntProperties>
                                 </configuration>
@@ -150,7 +156,7 @@
                         </executions>
                     </plugin>
 
-                    <!-- <plugin>
+                    <plugin>
                         <groupId>org.codehaus.mojo</groupId>
                         <artifactId>buildnumber-maven-plugin</artifactId>
                         <version>1.1</version>
@@ -162,7 +168,10 @@
                                 </goals>
                             </execution>
                         </executions>
-                    </plugin> -->
+                        <configuration>
+                            <scmDirectory>./..</scmDirectory>
+                        </configuration>
+                    </plugin>
                 </plugins>
             </build>
         </profile>
@@ -175,7 +184,7 @@
                 <!--<name>!vcsinfo</name>-->
                 <!--</property>-->
                 <file>
-                    <missing>${basedir}/.hg</missing>
+                    <missing>${basedir}/../.hg</missing>
                 </file>
             </activation>
 
@@ -265,6 +274,12 @@
                                     </includes>
                                 </filter>
                                 <filter>
+                                    <artifact>com.milaboratory:micommons</artifact>
+                                    <includes>
+                                        <include>**</include>
+                                    </includes>
+                                </filter>
+                                <filter>
                                     <artifact>*:*</artifact>
                                     <excludes>
                                         <exclude>META-INF/localization/*</exclude>
Binary files /tmp/5_yOnfIyun/mitcr-1.0.2/src/.DS_Store and /tmp/kGPchmFFbO/mitcr-1.0.3/src/.DS_Store differ
Binary files /tmp/5_yOnfIyun/mitcr-1.0.2/src/main/.DS_Store and /tmp/kGPchmFFbO/mitcr-1.0.3/src/main/.DS_Store differ
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/clone/CloneImpl.java mitcr-1.0.3/src/main/java/com/milaboratory/core/clone/CloneImpl.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/clone/CloneImpl.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/clone/CloneImpl.java	2013-10-09 08:03:10.000000000 +0000
@@ -39,7 +39,7 @@
  */
 public class CloneImpl implements Clone {
     protected final int id;
-    protected final NucleotideSQPair cdr3;
+    protected NucleotideSQPair cdr3;
     //V = 0; J = 1; D = 2
     protected final BitArray[] barcodes = new BitArray[3];
     protected int[] segmentCoords;
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/clone/CloneSet.java mitcr-1.0.3/src/main/java/com/milaboratory/core/clone/CloneSet.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/clone/CloneSet.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/clone/CloneSet.java	2013-10-09 08:03:10.000000000 +0000
@@ -34,7 +34,7 @@
  * @author Bolotin Dmitriy (bolotin.dmitriy@gmail.com)
  * @author Shugay Mikhail (mikhail.shugay@gmail.com)
  */
-public interface CloneSet {
+public interface CloneSet extends Iterable<Clone> {
     /**
      * Gets total number of CDR3-containing sequences in dataset
      *
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/clone/CloneSetImpl.java mitcr-1.0.3/src/main/java/com/milaboratory/core/clone/CloneSetImpl.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/clone/CloneSetImpl.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/clone/CloneSetImpl.java	2013-10-09 08:03:10.000000000 +0000
@@ -100,6 +100,11 @@
     }
 
     @Override
+    public Iterator<Clone> iterator() {
+        return (Iterator) clones.iterator();
+    }
+
+    @Override
     public SegmentGroupContainer getSegmentGroupContainer(SegmentGroupType type) {
         return segmentContainers[type.id()];
     }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/io/CloneSetIO.java mitcr-1.0.3/src/main/java/com/milaboratory/core/io/CloneSetIO.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/io/CloneSetIO.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/io/CloneSetIO.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,266 @@
+/*
+ * MiTCR <http://milaboratory.com>
+ *
+ * Copyright (c) 2010-2013:
+ *     Bolotin Dmitriy     <bolotin.dmitriy@gmail.com>
+ *     Chudakov Dmitriy    <chudakovdm@mail.ru>
+ *
+ * MiTCR is free software: you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+package com.milaboratory.core.io;
+
+import com.milaboratory.core.clone.Clone;
+import com.milaboratory.core.clone.CloneImpl;
+import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.core.clone.CloneSetImpl;
+import com.milaboratory.core.segment.*;
+import com.milaboratory.core.sequence.NucleotideSQPair;
+import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
+import com.milaboratory.core.sequence.quality.QualityFormat;
+import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
+import com.milaboratory.mitcr.cli.ExportDetalizationLevel;
+import com.milaboratory.mitcr.cli.ParametersIO;
+import com.milaboratory.mitcr.pipeline.Parameters;
+import com.milaboratory.util.BitArray;
+import com.milaboratory.util.CompressionType;
+import com.milaboratory.util.TablePrintStreamAdapter;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+
+public final class CloneSetIO {
+    public static final String CURRENT_FULL_MAGIC_PREFIX = "MiTCRFullExportV1.1";
+
+    private CloneSetIO() {
+    }
+
+    public static void printHeader(TablePrintStreamAdapter table, ExportDetalizationLevel detalization) {
+        switch (detalization) {
+            case Full:
+                table.row("Read count", "Percentage", "CDR3 nucleotide sequence", "CDR3 nucleotide quality", "Min quality",
+                        "CDR3 amino acid sequence", "V alleles", "V segments", "J alleles", "J segments",
+                        "D alleles", "D segments", "Last V nucleotide position ", "First D nucleotide position", "Last D nucleotide position",
+                        "First J nucleotide position", "VD insertions", "DJ insertions", "Total insertions");
+                return;
+            case Medium:
+                table.row("Read count", "Percentage", "CDR3 nucleotide sequence",
+                        "CDR3 amino acid sequence", "V segments", "J segments",
+                        "D segments", "Last V nucleotide position ", "First D nucleotide position", "Last D nucleotide position",
+                        "First J nucleotide position", "VD insertions", "DJ insertions", "Total insertions");
+                return;
+            case Simple:
+                table.row("Read count", "Percentage", "CDR3 nucleotide sequence",
+                        "CDR3 amino acid sequence", "V segments", "J segments",
+                        "D segments");
+                return;
+        }
+    }
+
+    public static void printClone(TablePrintStreamAdapter table, Clone clone, ExportDetalizationLevel detalization) {
+        switch (detalization) {
+            case Full:
+                table.row(clone.getCount(), clone.getPart(), clone.getCDR3().getSequence(), clone.getCDR3().getQuality(),
+                        clone.getCDR3().getQuality().minValue(),
+                        clone.getCDR3AA(), clone.getVAlleles(), clone.getVSegments(), clone.getJAlleles(), clone.getJSegments(),
+                        clone.getDAlleles(), clone.getDSegments(), clone.getVEnd(), clone.getDStart(), clone.getDEnd(),
+                        clone.getJStart(), clone.insertionsVD(), clone.insertionsDJ(), clone.insertionsTotal());
+                return;
+            case Medium:
+                table.row(clone.getCount(), clone.getPart(), clone.getCDR3().getSequence(),
+                        clone.getCDR3AA(), clone.getVSegments(), clone.getJSegments(),
+                        clone.getDSegments(), clone.getVEnd(), clone.getDStart(), clone.getDEnd(),
+                        clone.getJStart(), clone.insertionsVD(), clone.insertionsDJ(), clone.insertionsTotal());
+                return;
+            case Simple:
+                table.row(clone.getCount(), clone.getPart(), clone.getCDR3().getSequence(),
+                        clone.getCDR3AA(), clone.getVSegments(), clone.getJSegments(),
+                        clone.getDSegments());
+        }
+    }
+
+    public static void exportCloneSet(TablePrintStreamAdapter table, CloneSet cloneSet,
+                                      ExportDetalizationLevel detalization) {
+        exportCloneSet(table, cloneSet, detalization, null, null);
+    }
+
+    public static void exportCloneSet(TablePrintStreamAdapter table, CloneSet cloneSet,
+                                      ExportDetalizationLevel detalization, Parameters params, String inputAddress) {
+        if (detalization == ExportDetalizationLevel.Full) {
+            table.row(CURRENT_FULL_MAGIC_PREFIX, cloneSet.getSpecies().name(),
+                    cloneSet.getGene().getXmlRepresentation(), inputAddress,
+                    params == null ?
+                            null : ParametersIO.exportParametersToString(params));
+        }
+        printHeader(table, detalization);
+        for (Clone clone : cloneSet.getClones())
+            printClone(table, clone, detalization);
+    }
+
+    public static void exportCloneSet(PrintStream stream, CloneSet cloneSet,
+                                      ExportDetalizationLevel detalization) {
+        exportCloneSet(stream, cloneSet, detalization, null, null);
+    }
+
+    public static void exportCloneSet(PrintStream stream, CloneSet cloneSet,
+                                      ExportDetalizationLevel detalization, Parameters params, String inputAddress) {
+        exportCloneSet(new TablePrintStreamAdapter(stream), cloneSet, detalization, params, inputAddress);
+    }
+
+    public static void exportCloneSet(String fileName, CloneSet cloneSet,
+                                      ExportDetalizationLevel detalization, CompressionType ct) throws IOException {
+        exportCloneSet(fileName, cloneSet, detalization, null, null, ct);
+    }
+
+    public static void exportCloneSet(String fileName, CloneSet cloneSet,
+                                      ExportDetalizationLevel detalization, Parameters params, String inputAddress, CompressionType ct) throws IOException {
+        try (PrintStream ps = new PrintStream(ct.createOutputStream(new FileOutputStream(fileName)))) {
+            exportCloneSet(ps, cloneSet, detalization, params, inputAddress);
+        }
+    }
+
+    //TODO fix
+
+    /**
+     * Reads clone set formatted as tab-delimited table using {@link com.milaboratory.core.io.CloneSetIO#exportCloneSet(String,
+     * com.milaboratory.core.clone.CloneSet, ExportDetalizationLevel)} with detalization level equals to {@link
+     * ExportDetalizationLevel#Full}.
+     *
+     * @param fileName file name
+     * @return resulting clone set
+     */
+    public static CloneSet importCloneSet(String fileName) throws IOException {
+        CompressionType ct = CompressionType.None;
+        if (fileName.endsWith(".gz"))
+            ct = CompressionType.GZIP;
+        return importCloneSet(new FileInputStream(fileName), ct);
+    }
+
+    public static CloneSet importCloneSet(InputStream stream) throws IOException {
+        return importCloneSet(stream, CompressionType.None);
+    }
+
+    public static CloneSet importCloneSet(InputStream stream, CompressionType ct) throws IOException {
+        return importCloneSet(ct.createInputStream(stream), DefaultSegmentLibrary.load());
+    }
+
+    public static CloneSet importCloneSet(InputStream stream, SegmentLibrary library) throws IOException {
+
+        BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
+
+        String line = reader.readLine();
+
+        //Checking MagicPrefix
+        int format = -1;
+        if (line.startsWith(CloneSetIO.CURRENT_FULL_MAGIC_PREFIX))
+            format = 1;
+
+        if (line.startsWith("MiTCRFullExportV1.0"))
+            format = 0;
+
+        if (format == -1)
+            throw new IOException("Wrong file format.");
+
+        String[] splitLine = line.split("\t");
+
+        //Retrieving gene and species from header
+        Species species;
+        try {
+            species = Species.valueOf(splitLine[1]);
+        } catch (IllegalArgumentException iae) {
+            throw new IOException("Wrong file format.");
+        }
+        Gene gene = Gene.fromXML(splitLine[2]);
+        if (gene == null)
+            throw new IOException("Wrong file format.");
+
+        //Redundant check
+        if ((splitLine = reader.readLine().split("\t")).length != 19)
+            throw new IOException("Bad number of columns in header.");
+
+        /*
+            Format summary:
+
+                0 clone.getCount(),
+                1 clone.getPart(),
+                2 clone.getCDR3().getSequence(),
+                3 clone.getCDR3().getQuality(),
+                4 clone.getCDR3().getQuality().minValue(),
+                5 clone.getCDR3AA(),
+                6 clone.getVAlleles(),
+                7 clone.getVSegments(),
+                8 clone.getJAlleles(),
+                9 clone.getJSegments(),
+                10 clone.getDAlleles(),
+                11 clone.getDSegments(),
+                12 clone.getVEnd(),
+                13 clone.getDStart(),
+                14 clone.getDEnd(),
+                15 clone.getJStart(),
+                16 clone.insertionsVD(),
+                17 clone.insertionsDJ(),
+                18 clone.insertionsTotal()
+        */
+
+
+        int id = 0;
+
+        //SegmentLibrary library = DefaultSegmentLibrary.load();
+        final SegmentGroupContainer vContainer = library.getGroup(species, gene, SegmentGroupType.Variable),
+                jContainer = library.getGroup(species, gene, SegmentGroupType.Joining),
+                dContainer = gene.hasDSegment() ? library.getGroup(species, gene, SegmentGroupType.Diversity) : null;
+
+        List<Clone> clones = new ArrayList<>();
+        CloneImpl clone;
+        while ((line = reader.readLine()) != null) {
+            splitLine = line.split("\t");
+
+            //Retrieving reads count
+            long count = Long.parseLong(splitLine[0]);
+
+            //Retrieving segments for current clone
+            BitArray vBarcode = new BitArray(vContainer.getAllelesCount());
+            for (String vSegmentName : splitLine[6].split(","))
+                vBarcode.set(vContainer.getAlleleByName(vSegmentName.trim()).getIndex());
+
+            BitArray jBarcode = new BitArray(jContainer.getAllelesCount());
+            for (String jSegmentName : splitLine[8].split(","))
+                jBarcode.set(jContainer.getAlleleByName(jSegmentName.trim()).getIndex());
+
+            BitArray dBarcode = null;
+            if (dContainer != null) {
+                dBarcode = new BitArray(dContainer.getAllelesCount());
+                if (!splitLine[10].isEmpty())
+                    for (String dSegment : splitLine[10].split(","))
+                        dBarcode.set(dContainer.getAlleleByName(dSegment.trim()).getIndex());
+            }
+            BitArray[] segmentBarcodes = new BitArray[]{vBarcode, jBarcode, dBarcode};
+
+            //Retrieving segments layout for current clone
+            int[] segmentCoords;
+            if (Integer.parseInt(splitLine[13]) > -1)
+                segmentCoords = new int[]{Integer.parseInt(splitLine[12]), Integer.parseInt(splitLine[13]),
+                        Integer.parseInt(splitLine[14]), Integer.parseInt(splitLine[15])};
+            else
+                segmentCoords = new int[]{Integer.parseInt(splitLine[12]), Integer.parseInt(splitLine[15])};
+
+            clone = new CloneImpl(id++, new NucleotideSQPair(new NucleotideSequence(splitLine[2]),
+                    new SequenceQualityPhred(splitLine[3], QualityFormat.Phred33)), count, segmentBarcodes, segmentCoords);
+            clones.add(clone);
+        }
+
+        //Creating clone set
+        return new CloneSetImpl<>(clones, gene, species, vContainer, jContainer, dContainer);
+    }
+}
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/util/CloneSetsComparator.java mitcr-1.0.3/src/main/java/com/milaboratory/core/util/CloneSetsComparator.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/util/CloneSetsComparator.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/util/CloneSetsComparator.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,37 @@
+package com.milaboratory.core.util;
+
+import com.milaboratory.core.clone.Clone;
+import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
+
+import java.util.HashMap;
+
+public class CloneSetsComparator {
+    public static final CloneSetsComparisonResult compare(CloneSet csFrom, CloneSet csTo) {
+        int mClones = 0, nClones = 0, mSequences = 0, nSequences = 0;
+        Clone cFrom;
+
+        //Adding all from clone to has map
+        HashMap<NucleotideSequence, Clone> fromClones = new HashMap<>(csFrom.getClones().size());
+        for (Clone clone : csFrom)
+            fromClones.put(clone.getCDR3().getSequence(), clone);
+
+        for (Clone cTo : csTo) {
+            cFrom = fromClones.remove(cTo.getCDR3().getSequence());
+            if (cFrom == null) {
+                ++nClones;
+                nSequences += cTo.getCount();
+            }
+        }
+        mClones = fromClones.size();
+        for (Clone clone : fromClones.values())
+            mSequences += clone.getCount();
+
+        assert csFrom.getClones().size() + nClones - mClones == csTo.getClones().size();
+        assert csFrom.getTotalCount() + nSequences - mSequences == csTo.getTotalCount();
+
+        double difference = 1.0 * (nSequences + mSequences) / (csFrom.getTotalCount() + csTo.getTotalCount());
+
+        return new CloneSetsComparisonResult(nClones, mClones, nSequences, mSequences, difference);
+    }
+}
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/util/CloneSetsComparisonResult.java mitcr-1.0.3/src/main/java/com/milaboratory/core/util/CloneSetsComparisonResult.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/util/CloneSetsComparisonResult.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/util/CloneSetsComparisonResult.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,14 @@
+package com.milaboratory.core.util;
+
+public class CloneSetsComparisonResult {
+    public final int newClones, missedClones, newSequences, missedSequences;
+    public final double difference;
+
+    public CloneSetsComparisonResult(int newClones, int missedClones, int newSequences, int missedSequences, double difference) {
+        this.newClones = newClones;
+        this.missedClones = missedClones;
+        this.newSequences = newSequences;
+        this.missedSequences = missedSequences;
+        this.difference = difference;
+    }
+}
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/core/util/CompareCloneSets.java mitcr-1.0.3/src/main/java/com/milaboratory/core/util/CompareCloneSets.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/core/util/CompareCloneSets.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/core/util/CompareCloneSets.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,24 @@
+package com.milaboratory.core.util;
+
+import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.core.io.CloneSetIO;
+
+public class CompareCloneSets {
+    public static void main(String[] args) throws Exception {
+        CloneSet cs1 = CloneSetIO.importCloneSet(args[1]),
+                cs2 = CloneSetIO.importCloneSet(args[2]);
+        CloneSetsComparisonResult result = CloneSetsComparator.compare(cs1, cs2);
+
+        switch (args[0]) {
+            case "d":
+                System.out.println(result.difference);
+                break;
+            case "v":
+                System.out.println("Clones: +" + result.newClones +
+                        " | -" + result.missedClones + "");
+                System.out.println("Sequences: +" + result.newSequences +
+                        " | -" + result.missedSequences);
+                System.out.println("Difference = " + result.difference);
+        }
+    }
+}
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/SimpleTest.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/SimpleTest.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/SimpleTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/SimpleTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -24,8 +24,8 @@
 import com.milaboratory.core.clone.CloneSetClustered;
 import com.milaboratory.core.segment.Gene;
 import com.milaboratory.core.segment.Species;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractorParameters;
 import com.milaboratory.mitcr.cdrextraction.Strand;
 import com.milaboratory.mitcr.clonegenerator.LQMappingCloneGeneratorParameters;
@@ -52,11 +52,12 @@
 
         SFastqReader reads = new SFastqReader(input,
                 args.length > 1 ?
-                        QualityStringFormat.Illumina13 : QualityStringFormat.Illumina18, compressionType);
+                        QualityFormat.Phred33 : QualityFormat.Phred64, compressionType);
 
         new Thread(new ProgressReporter("Processing sequences: ", reads)).start();
 
-        Parameters parameters = new Parameters(Gene.TRB, Species.HomoSapiens, new CDR3ExtractorParameters(new VJSegmentMapperParameters(AlignmentDirection.Both, -4, 1, 12, 3),
+        Parameters parameters = new Parameters(Gene.TRB, Species.HomoSapiens,
+                new CDR3ExtractorParameters(new VJSegmentMapperParameters(AlignmentDirection.Both, -4, 1, 12, 3),
                 new VJSegmentMapperParameters(AlignmentDirection.InsideCDR3, -3, 2, 7, -2),
                 //new VJSegmentMapperParameters(-1, 4, 12, -2, AlignmentDirection.TrivialAlignment),
                 new DSegmentMapperParameters(6), Strand.Both, true));
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cdrextraction/CoreCDR3Extractor.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cdrextraction/CoreCDR3Extractor.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cdrextraction/CoreCDR3Extractor.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cdrextraction/CoreCDR3Extractor.java	2013-10-09 08:03:10.000000000 +0000
@@ -59,7 +59,7 @@
         if (phe < cys)
             return null;
         try {
-            return data.getSubPairCopy(cys, phe + 1).getDeepCopy();
+            return data.getRange(cys, phe + 1);
         } catch (IndexOutOfBoundsException ex) {  //Very rear event, so Exception usage in this place does make sense.
             return null;
         }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/BuildInformation.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/BuildInformation.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/BuildInformation.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/BuildInformation.java	2013-10-09 08:03:10.000000000 +0000
@@ -21,7 +21,7 @@
 package com.milaboratory.mitcr.cli;
 
 public class BuildInformation {
-    String scmChangeset, scmDate, scmBranch, version, jdk, builtBy, buildDate;
+    public final String scmChangeset, scmDate, scmBranch, version, jdk, builtBy, buildDate;
 
     public BuildInformation(String scmChangeset, String scmDate, String scmBranch, String version, String jdk, String builtBy, String buildDate) {
         this.scmChangeset = scmChangeset;
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/BuildInformationProvider.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/BuildInformationProvider.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/BuildInformationProvider.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/BuildInformationProvider.java	2013-10-09 08:03:10.000000000 +0000
@@ -52,10 +52,17 @@
             }
         } catch (Exception e) {
             e.printStackTrace();
-            System.out.println("SS1");
+            //System.out.println("SS1");
             return null;
         }
-        System.out.println("SS2");
+        //System.out.println("SS2");
         return null;
     }
+
+    public static String getVersion() {
+        BuildInformation buildInformation = get();
+        if (buildInformation == null)
+            return null;
+        return buildInformation.version;
+    }
 }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/Main.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/Main.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/Main.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/Main.java	2013-10-09 08:03:10.000000000 +0000
@@ -23,12 +23,13 @@
 import cc.redberry.pipe.OutputPort;
 import cc.redberry.pipe.util.CountLimitingOutputPort;
 import com.milaboratory.core.clone.CloneSetClustered;
+import com.milaboratory.core.io.CloneSetIO;
 import com.milaboratory.core.segment.DefaultSegmentLibrary;
 import com.milaboratory.core.segment.Gene;
 import com.milaboratory.core.segment.SegmentLibrary;
 import com.milaboratory.core.segment.Species;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.clonegenerator.AccumulatorType;
 import com.milaboratory.mitcr.clonegenerator.BasicCloneGeneratorParameters;
@@ -70,7 +71,8 @@
             LIMIT_OPTION = "limit",
             REPORT_OPTION = "report",
             REPORTING_LEVEL_OPTION = "level",
-            SOLEXA_OPTION = "solexa",
+            PHRED33_OPTION = "phred33",
+            PHRED64_OPTION = "phred64",
             INCLUDE_CYS_PHE_OPTION = "cysphe",
             PRINT_DEBUG_OPTION = "debug",
             PRINT_VERSION_OPTION = "v",
@@ -100,16 +102,16 @@
         orderingMap.put(EXPORT_OPTION, o++);
         orderingMap.put(REPORT_OPTION, o++);
         orderingMap.put(REPORTING_LEVEL_OPTION, o++);
-        orderingMap.put(SOLEXA_OPTION, o++);
+        orderingMap.put(PHRED33_OPTION, o++);
+        orderingMap.put(PHRED64_OPTION, o++);
         orderingMap.put(THREADS_OPTION, o++);
         orderingMap.put(COMPRESSED_OPTION, o++);
         orderingMap.put(PRINT_HELP_OPTION, o++);
         orderingMap.put(PRINT_VERSION_OPTION, o++);
         orderingMap.put(PRINT_DEBUG_OPTION, o++);
 
-
         options.addOption(OptionBuilder.withArgName("preset name")
-                .hasArg().withDescription("set of pipeline parameters to use")
+                .hasArg().withDescription("preset of pipeline parameters to use")
                 .create(PARAMETERS_SET_OPTION));
 
         options.addOption(OptionBuilder.withArgName("species")
@@ -174,8 +176,14 @@
                 .create(REPORTING_LEVEL_OPTION));
 
         options.addOption(OptionBuilder
-                .hasArg(false).withDescription("if input file is in old illumina format with 64 byte offset for quality string")
-                .create(SOLEXA_OPTION));
+                .hasArg(false).withDescription("add this option if input file is in old illumina format with 64 byte offset for quality " +
+                        "string (MiTCR will try to automatically detect file format if one of the \"-phredXX\" options is not provided)")
+                .create(PHRED64_OPTION));
+
+        options.addOption(OptionBuilder
+                .hasArg(false).withDescription("add this option if input file is in Phred+33 format for quality values " +
+                        "(MiTCR will try to automatically detect file format if one of the \"-phredXX\" options is not provided)")
+                .create(PHRED33_OPTION));
 
         options.addOption(OptionBuilder.withArgName("threads")
                 .hasArg().withDescription("specifies the number of CDR3 extraction threads (default = number of available CPU cores)")
@@ -359,20 +367,30 @@
                 return;
             }
 
+            //TODO This also done inside SFastqReader constructor
             CompressionType compressionType = CompressionType.None;
             if (inputFileName.endsWith(".gz"))
                 compressionType = CompressionType.GZIP;
 
-            QualityStringFormat format = QualityStringFormat.Illumina18;
-            if (cl.hasOption(SOLEXA_OPTION))
-                format = QualityStringFormat.Illumina13;
+            QualityFormat format = null; // If variable remains null file format will be detected automatically
+            if (cl.hasOption(PHRED33_OPTION))
+                format = QualityFormat.Phred33;
+            if (cl.hasOption(PHRED64_OPTION))
+                if (format == null)
+                    format = QualityFormat.Phred64;
+                else {
+                    err.println("Options: -" + PHRED33_OPTION + " and -" + PHRED64_OPTION + " are mutually exclusive");
+                    return;
+                }
+
 
-            SFastqReader reads = new SFastqReader(input,
-                    format, compressionType);
+            SFastqReader reads = format == null ?
+                    new SFastqReader(input, compressionType) :
+                    new SFastqReader(input, format, compressionType);
 
             OutputPort<SSequencingRead> inputToPipeline = reads;
             if (input_limit >= 0)
-                inputToPipeline = new CountLimitingOutputPort<SSequencingRead>(inputToPipeline, input_limit);
+                inputToPipeline = new CountLimitingOutputPort<>(inputToPipeline, input_limit);
 
             SegmentLibrary library = DefaultSegmentLibrary.load();
 
@@ -382,7 +400,7 @@
             pipeline.setThreads(threads);
             pipeline.setAnalysisListener(statisticsAggregator);
 
-            new Thread(new SmartProgressReporter(pipeline, err)).start();
+            new Thread(new SmartProgressReporter(pipeline, err)).start(); // Printing status to the standard error stream
 
             pipeline.run();
 
@@ -419,13 +437,13 @@
                 CompressionType compressionType1 = CompressionType.None;
                 if (outputFileName.endsWith(".gz"))
                     compressionType1 = CompressionType.GZIP;
-                TabDelimitedExporter.exportCloneSet(outputFileName, cloneSet, detalization, compressionType1);
+                CloneSetIO.exportCloneSet(outputFileName, cloneSet, detalization, params, input.getAbsolutePath(), compressionType1);
             }
         } catch (ParseException | RuntimeException | IOException e) {
-            e.printStackTrace();
-            err.println("Error occurred  while parsing parameters.");
+            err.println("Error occurred in the analysis pipeline.");
             err.println();
-            printHelp();
+            e.printStackTrace();
+            //printHelp();
         }
     }
 
@@ -439,9 +457,9 @@
             }
         });
         final String executable = System.getProperty("executable", "java -jar mitcr.jar");
-        err.println("usage: " + executable + " -preset <preset name> [options] input_file output_file.cls");
-        err.println("       " + executable + " -preset <preset name> [options] input_file output_file.txt");
-        err.println("       " + executable + " -preset <preset name> [options] -export newPresetName");
+        err.println("usage: " + executable + " -pset <preset name> [options] input_file output_file.cls");
+        err.println("       " + executable + " -pset <preset name> [options] input_file output_file.txt");
+        err.println("       " + executable + " -pset <preset name> [options] -export newPresetName");
         err.println();
 
         formatter.printOptions(new PrintWriter(err, true), 85, options, 2, 3);
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/ParametersIO.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/ParametersIO.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/ParametersIO.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/ParametersIO.java	2013-10-09 08:03:10.000000000 +0000
@@ -31,8 +31,24 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.StringReader;
 
 public class ParametersIO {
+    public static String exportParametersToString(Parameters parameters) {
+        Format format = Format.getCompactFormat();
+        return new XMLOutputter(format).outputString(parameters.asXML());
+    }
+
+    public static Parameters importParametersFromString(String string) {
+        try {
+            SAXBuilder builder = new SAXBuilder();
+            Document document = builder.build(new StringReader(string));
+            return Parameters.fromXML(document.getRootElement());
+        } catch (JDOMException | IOException ae) {
+            throw new RuntimeException(ae);
+        }
+    }
+
     public static void exportParameters(Parameters parameters, String fileName) {
         Format format = Format.getPrettyFormat();
         format.setLineSeparator("\n");
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedExporter.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedExporter.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedExporter.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedExporter.java	1970-01-01 00:00:00.000000000 +0000
@@ -1,103 +0,0 @@
-/*
- * MiTCR <http://milaboratory.com>
- *
- * Copyright (c) 2010-2013:
- *     Bolotin Dmitriy     <bolotin.dmitriy@gmail.com>
- *     Chudakov Dmitriy    <chudakovdm@mail.ru>
- *
- * MiTCR is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option)
- * any later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
- * more details.
- *
- * You should have received a copy of the GNU General Public License along
- * with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-package com.milaboratory.mitcr.cli;
-
-import com.milaboratory.core.clone.Clone;
-import com.milaboratory.core.clone.CloneSet;
-import com.milaboratory.util.CompressionType;
-import com.milaboratory.util.TablePrintStreamAdapter;
-
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.PrintStream;
-
-public final class TabDelimitedExporter {
-    public static final String FULL_MAGIC_PREFIX = "MiTCRFullExportV1.0";
-
-    private TabDelimitedExporter() {
-    }
-
-    public static void printHeader(TablePrintStreamAdapter table, ExportDetalizationLevel detalization) {
-        switch (detalization) {
-            case Full:
-                table.row("Read count", "Percentage", "CDR3 nucleotide sequence", "CDR3 nucleotide quality", "Min quality",
-                        "CDR3 amino acid sequence", "V alleles", "V segments", "J alleles", "J segments",
-                        "D alleles", "D segments", "Last V nucleotide position ", "First D nucleotide position", "Last D nucleotide position",
-                        "First J nucleotide position", "VD insertions", "DJ insertions", "Total insertions");
-                return;
-            case Medium:
-                table.row("Read count", "Percentage", "CDR3 nucleotide sequence",
-                        "CDR3 amino acid sequence", "V segments", "J segments",
-                        "D segments", "Last V nucleotide position ", "First D nucleotide position", "Last D nucleotide position",
-                        "First J nucleotide position", "VD insertions", "DJ insertions", "Total insertions");
-                return;
-            case Simple:
-                table.row("Read count", "Percentage", "CDR3 nucleotide sequence",
-                        "CDR3 amino acid sequence", "V segments", "J segments",
-                        "D segments");
-                return;
-        }
-    }
-
-    public static void printClone(TablePrintStreamAdapter table, Clone clone, ExportDetalizationLevel detalization) {
-        switch (detalization) {
-            case Full:
-                table.row(clone.getCount(), clone.getPart(), clone.getCDR3().getSequence(), clone.getCDR3().getQuality(),
-                        clone.getCDR3().getQuality().minRawQuality(),
-                        clone.getCDR3AA(), clone.getVAlleles(), clone.getVSegments(), clone.getJAlleles(), clone.getJSegments(),
-                        clone.getDAlleles(), clone.getDSegments(), clone.getVEnd(), clone.getDStart(), clone.getDEnd(),
-                        clone.getJStart(), clone.insertionsVD(), clone.insertionsDJ(), clone.insertionsTotal());
-                return;
-            case Medium:
-                table.row(clone.getCount(), clone.getPart(), clone.getCDR3().getSequence(),
-                        clone.getCDR3AA(), clone.getVSegments(), clone.getJSegments(),
-                        clone.getDSegments(), clone.getVEnd(), clone.getDStart(), clone.getDEnd(),
-                        clone.getJStart(), clone.insertionsVD(), clone.insertionsDJ(), clone.insertionsTotal());
-                return;
-            case Simple:
-                table.row(clone.getCount(), clone.getPart(), clone.getCDR3().getSequence(),
-                        clone.getCDR3AA(), clone.getVSegments(), clone.getJSegments(),
-                        clone.getDSegments());
-        }
-    }
-
-    public static void exportCloneSet(TablePrintStreamAdapter table, CloneSet cloneSet, ExportDetalizationLevel detalization) {
-        if (detalization == ExportDetalizationLevel.Full)
-            table.row(FULL_MAGIC_PREFIX, cloneSet.getSpecies().name(), cloneSet.getGene().getXmlRepresentation());
-        printHeader(table, detalization);
-        for (Clone clone : cloneSet.getClones())
-            printClone(table, clone, detalization);
-    }
-
-    public static void exportCloneSet(PrintStream stream, CloneSet cloneSet, ExportDetalizationLevel detalization) {
-        exportCloneSet(new TablePrintStreamAdapter(stream), cloneSet, detalization);
-    }
-
-    public static void exportCloneSet(String fileName, CloneSet cloneSet, ExportDetalizationLevel detalization) throws IOException {
-        exportCloneSet(fileName, cloneSet, detalization, CompressionType.None);
-    }
-
-    public static void exportCloneSet(String fileName, CloneSet cloneSet, ExportDetalizationLevel detalization, CompressionType ct) throws IOException {
-        try (PrintStream ps = new PrintStream(ct.createOutputStream(new FileOutputStream(fileName)))) {
-            exportCloneSet(ps, cloneSet, detalization);
-        }
-    }
-}
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedImporter.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedImporter.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedImporter.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/cli/TabDelimitedImporter.java	1970-01-01 00:00:00.000000000 +0000
@@ -1,168 +0,0 @@
-/*
- * MiTCR <http://milaboratory.com>
- *
- * Copyright (c) 2010-2013:
- *     Bolotin Dmitriy     <bolotin.dmitriy@gmail.com>
- *     Chudakov Dmitriy    <chudakovdm@mail.ru>
- *
- * MiTCR is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option)
- * any later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
- * more details.
- *
- * You should have received a copy of the GNU General Public License along
- * with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-package com.milaboratory.mitcr.cli;
-
-import com.milaboratory.core.clone.Clone;
-import com.milaboratory.core.clone.CloneImpl;
-import com.milaboratory.core.clone.CloneSet;
-import com.milaboratory.core.clone.CloneSetImpl;
-import com.milaboratory.core.segment.*;
-import com.milaboratory.core.sequence.NucleotideSQPair;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
-import com.milaboratory.util.BitArray;
-import com.milaboratory.util.CompressionType;
-
-import java.io.*;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * 1/7/13 MS (mikhail.shugay@gmail.com)
- */
-public final class TabDelimitedImporter {
-    private TabDelimitedImporter() {
-    }
-
-    /**
-     * Reads clone set formatted as tab-delimited table using {@link TabDelimitedExporter#exportCloneSet(String,
-     * com.milaboratory.core.clone.CloneSet, ExportDetalizationLevel)} with detalization level equals to {@link
-     * ExportDetalizationLevel#Full}.
-     *
-     * @param fileName file name
-     * @return resulting clone set
-     */
-    public static CloneSet importCloneSet(String fileName) throws IOException {
-        CompressionType ct = CompressionType.None;
-        if (fileName.endsWith(".gz"))
-            ct = CompressionType.GZIP;
-        return importCloneSet(ct.createInputStream(new FileInputStream(fileName)));
-    }
-
-    public static CloneSet importCloneSet(InputStream stream) throws IOException {
-        return importCloneSet(stream, DefaultSegmentLibrary.load());
-    }
-
-    public static CloneSet importCloneSet(InputStream stream, SegmentLibrary library) throws IOException {
-
-        BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
-
-        String line = reader.readLine();
-
-        //Checking first bytes
-        if (!line.startsWith(TabDelimitedExporter.FULL_MAGIC_PREFIX))
-            throw new IOException("Wrong file format.");
-
-        String[] splitLine = line.split("\t");
-
-        //Retrieving gene and species from header
-        Species species;
-        try {
-            species = Species.valueOf(splitLine[1]);
-        } catch (IllegalArgumentException iae) {
-            throw new IOException("Wrong file format.");
-        }
-        Gene gene = Gene.fromXML(splitLine[2]);
-        if (gene == null)
-            throw new IOException("Wrong file format.");
-
-        //Redundant check
-        if ((splitLine = reader.readLine().split("\t")).length != 19)
-            throw new IOException("Bad number of columns in header.");
-
-        /*
-            Format summary:
-
-                0 clone.getCount(),
-                1 clone.getPart(),
-                2 clone.getCDR3().getSequence(),
-                3 clone.getCDR3().getQuality(),
-                4 clone.getCDR3().getQuality().minRawQuality(),
-                5 clone.getCDR3AA(),
-                6 clone.getVAlleles(),
-                7 clone.getVSegments(),
-                8 clone.getJAlleles(),
-                9 clone.getJSegments(),
-                10 clone.getDAlleles(),
-                11 clone.getDSegments(),
-                12 clone.getVEnd(),
-                13 clone.getDStart(),
-                14 clone.getDEnd(),
-                15 clone.getJStart(),
-                16 clone.insertionsVD(),
-                17 clone.insertionsDJ(),
-                18 clone.insertionsTotal()
-        */
-
-
-        //Std Sanger quality format with 33 offset
-        final QualityStringFormat format = QualityStringFormat.Illumina18u;
-
-        int id = 0;
-
-        //SegmentLibrary library = DefaultSegmentLibrary.load();
-        final SegmentGroupContainer vContainer = library.getGroup(species, gene, SegmentGroupType.Variable),
-                jContainer = library.getGroup(species, gene, SegmentGroupType.Joining),
-                dContainer = gene.hasDSegment() ? library.getGroup(species, gene, SegmentGroupType.Diversity) : null;
-
-        List<Clone> clones = new ArrayList<>();
-        CloneImpl clone;
-        while ((line = reader.readLine()) != null) {
-            splitLine = line.split("\t");
-
-            //Retrieving reads count
-            long count = Long.parseLong(splitLine[0]);
-
-            //Retrieving segments for current clone
-            BitArray vBarcode = new BitArray(vContainer.getAllelesCount());
-            for (String vSegmentName : splitLine[6].split(","))
-                vBarcode.set(vContainer.getAlleleByName(vSegmentName.trim()).getIndex());
-
-            BitArray jBarcode = new BitArray(jContainer.getAllelesCount());
-            for (String jSegmentName : splitLine[8].split(","))
-                jBarcode.set(jContainer.getAlleleByName(jSegmentName.trim()).getIndex());
-
-            BitArray dBarcode = null;
-            if (dContainer != null) {
-                dBarcode = new BitArray(dContainer.getAllelesCount());
-                if (!splitLine[10].isEmpty())
-                    for (String dSegment : splitLine[10].split(","))
-                        dBarcode.set(dContainer.getAlleleByName(dSegment.trim()).getIndex());
-            }
-            BitArray[] segmentBarcodes = new BitArray[]{vBarcode, jBarcode, dBarcode};
-
-            //Retrieving segments layout for current clone
-            int[] segmentCoords;
-            if (Integer.parseInt(splitLine[13]) > -1)
-                segmentCoords = new int[]{Integer.parseInt(splitLine[12]), Integer.parseInt(splitLine[13]),
-                        Integer.parseInt(splitLine[14]), Integer.parseInt(splitLine[15])};
-            else
-                segmentCoords = new int[]{Integer.parseInt(splitLine[12]), Integer.parseInt(splitLine[15])};
-
-            clone = new CloneImpl(id++, new NucleotideSQPair(NucleotideSequenceImpl.fromSequence(splitLine[2]),
-                    format.getQualityFactory().create(splitLine[3].getBytes())), count, segmentBarcodes, segmentCoords);
-            clones.add(clone);
-        }
-
-        //Creating clone set
-        return new CloneSetImpl<>(clones, gene, species, vContainer, jContainer, dContainer);
-    }
-}
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorClone.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorClone.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorClone.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorClone.java	2013-10-09 08:03:10.000000000 +0000
@@ -2,6 +2,7 @@
 
 import com.milaboratory.core.clone.CloneImpl;
 import com.milaboratory.core.sequence.NucleotideSQPair;
+import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
 import com.milaboratory.mitcr.vdjmapping.SegmentMappingResult;
 
@@ -12,9 +13,11 @@
 
 public abstract class AccumulatorClone extends CloneImpl {
     long additionalCount = 0;
+    final NucleotideSequence sequence;
 
     AccumulatorClone(int id, NucleotideSQPair cdr3, boolean saveLinks) {
-        super(id, cdr3);
+        super(id, null);
+        sequence = cdr3.getSequence();
         if (saveLinks)
             links = new ArrayList<>();
         else
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneAvrg.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneAvrg.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneAvrg.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneAvrg.java	2013-10-09 08:03:10.000000000 +0000
@@ -8,27 +8,33 @@
 import static com.milaboratory.mitcr.clonegenerator.AverageQualityCalculator.nextValues;
 
 public abstract class AccumulatorCloneAvrg extends AccumulatorClone {
+    byte[] accumulator;
+
     public AccumulatorCloneAvrg(int id, NucleotideSQPair cdr3, boolean saveLinks) {
         super(id, cdr3, saveLinks);
+        accumulator = new byte[cdr3.size()];
     }
 
     @Override
     synchronized void include(CDR3ExtractionResult result, boolean additional) {
         super.include(result, additional);
 
-        //Returns a link to the underlying byte array, so it could be used here for
-        //accumulation of average values
-        //IMPORTANT: because of this quality object of clone is invalid before clone compilation
-        final byte[] avrgStorage = ((SequenceQualityPhred) cdr3.getQuality()).getRawData();
+        ////Returns a link to the underlying byte array, so it could be used here for
+        ////accumulation of average values
+        ////IMPORTANT: because of this quality object of clone is invalid before clone compilation
+        //final byte[] avrgStorage = cdr3.getQuality().getInnerData();
 
         //Adding observed values
-        nextValues(avrgStorage, count - 1,
-                ((SequenceQualityPhred) result.getCDR3().getQuality()).getRawData());
+        nextValues(accumulator, count - 1,
+                result.getCDR3().getQuality().getInnerData());
     }
 
     @Override
     void compile(float barcodeAggregationFactor) {
         //Now the quality object is valid
-        convertValues(((SequenceQualityPhred) cdr3.getQuality()).getRawData());
+        //convertValues(cdr3.getQuality().getInnerData());
+        convertValues(accumulator);
+        cdr3 = new NucleotideSQPair(sequence, new SequenceQualityPhred(accumulator));
+        accumulator = null;
     }
 }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMax.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMax.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMax.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMax.java	2013-10-09 08:03:10.000000000 +0000
@@ -1,17 +1,31 @@
 package com.milaboratory.mitcr.clonegenerator;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
+import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
 
 public abstract class AccumulatorCloneMax extends AccumulatorClone {
+    final byte[] quality;
+
     public AccumulatorCloneMax(int id, NucleotideSQPair cdr3, boolean saveLinks) {
         super(id, cdr3, saveLinks);
+        quality = new byte[cdr3.size()];
     }
 
     @Override
     synchronized void include(CDR3ExtractionResult result, boolean additional) {
         super.include(result, additional);
 
-        cdr3.getQuality().mergeWith(result.getCDR3().getQuality());
+        byte val;
+        for (int i = 0; i < quality.length; ++i)
+            if (quality[i] < (val = result.getCDR3().getQuality().value(i)))
+                quality[i] = val;
+
+        //cdr3.getQuality().mergeWith(result.getCDR3().getQuality());
+    }
+
+    @Override
+    void compile(float barcodeAggregationFactor) {
+        cdr3 = new NucleotideSQPair(sequence, new SequenceQualityPhred(quality));
     }
 }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxCompressed.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxCompressed.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxCompressed.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxCompressed.java	2013-10-09 08:03:10.000000000 +0000
@@ -37,6 +37,9 @@
 
     @Override
     void compile(float barcodeAggregationFactor) {
+        //Needed to compile quality values
+        super.compile(barcodeAggregationFactor);
+
         for (int i = 0; i < 3; ++i)
             if (barcodeAccumulators[i] == null)
                 barcodes[i] = null;
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxStrict.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxStrict.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxStrict.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AccumulatorCloneMaxStrict.java	2013-10-09 08:03:10.000000000 +0000
@@ -62,6 +62,9 @@
 
     @Override
     void compile(float barcodeAggregationFactor) {
+        //Needed to compile quality values
+        super.compile(barcodeAggregationFactor);
+
         for (int i = 0; i < 3; ++i)
             if (bcAggregators[i] == null)
                 barcodes[i] = null;
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculator.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculator.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculator.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculator.java	2013-10-09 08:03:10.000000000 +0000
@@ -6,7 +6,7 @@
 public class AverageQualityCalculator {
     /**
      * This method is intended to calculate average value of sequence of numbers between 0 and 63 using only 1 byte of
-     * information. The only additional information is number of observations.
+     * information. The only additional information needed is a number of observations.
      *
      * <p>Performance: resulting value error with 95% probability will be: (1) less than 1 point for small sample sizes
      * and (2) less than 2.2 points for big samples. One iteration takes about 100 cycles on the Core i7 processor.</p>
@@ -69,7 +69,7 @@
     private static ThreadLocal<RandomGenerator> tlRandomGenerator = new ThreadLocal<RandomGenerator>() {
         @Override
         protected RandomGenerator initialValue() {
-            return new MersenneTwister();
+            return new MersenneTwister(75586L); //Fixed value for calculation reproducibility
         }
     };
 
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGenerator.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGenerator.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGenerator.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGenerator.java	2013-10-09 08:03:10.000000000 +0000
@@ -140,7 +140,7 @@
                         initializeFromResult(cdr3ExtractionResult);
 
                     node.clone = cloneFactory.create(this.clonesCount.getAndIncrement(),
-                            cdr3ExtractionResult.getCDR3().getDeepCopy(), saveBackwardLinks);
+                            cdr3ExtractionResult.getCDR3(), saveBackwardLinks);
 
                     //The new clone was created
                     created = true;
@@ -161,6 +161,19 @@
         return created;
     }
 
+    @Override
+    public final void preInitialize(SegmentGroupContainer v, SegmentGroupContainer j, SegmentGroupContainer d) {
+        segmentContainers.compareAndSet(0, null, v);
+        segmentContainers.compareAndSet(1, null, j);
+        gene.compareAndSet(null, v.getGroup().getGene());
+        if (gene.get().hasDSegment())
+            segmentContainers.compareAndSet(2, null, d);
+
+        initialized.set(segmentContainers.get(0) != null &&
+                segmentContainers.get(1) != null &&
+                (!gene.get().hasDSegment() || segmentContainers.get(2) != null));
+    }
+
     private void initializeFromResult(CDR3ExtractionResult result) {
         if (segmentContainers.get(0) == null) {
             segmentContainers.compareAndSet(0, null, result.getVMappingResult().getContainer());
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/CloneGenerator.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/CloneGenerator.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clonegenerator/CloneGenerator.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clonegenerator/CloneGenerator.java	2013-10-09 08:03:10.000000000 +0000
@@ -22,6 +22,7 @@
 
 import cc.redberry.pipe.InputPortUninterruptible;
 import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.core.segment.SegmentGroupContainer;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
 
 /**
@@ -32,6 +33,17 @@
  */
 public interface CloneGenerator extends InputPortUninterruptible<CDR3ExtractionResult<?>> {
     /**
+     * In normal conditions clone generator can get information about gene and particular set of gene segments from the
+     * input stream of extraction results, but in some conditions (if there where no CDR3s or no D segment was mapped)
+     * it requires explicit initialization usint this method.
+     *
+     * @param v segment group container for V segments
+     * @param j segment group container for J segments
+     * @param d segment group container for D segments
+     */
+    void preInitialize(SegmentGroupContainer v, SegmentGroupContainer j, SegmentGroupContainer d);
+
+    /**
      * Build and gets the resulting clone set. Should be called after this port is closed (null was put)
      *
      * @return set of generated clone
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSQPairIO.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSQPairIO.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSQPairIO.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSQPairIO.java	2013-10-09 08:03:10.000000000 +0000
@@ -20,11 +20,11 @@
  */
 package com.milaboratory.mitcr.clsexport.io.serializers;
 
+import com.milaboratory.core.sequence.NucleotideSQPair;
+import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
+import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 import com.milaboratory.mitcr.clsexport.io.BinaryContainerReader;
 import com.milaboratory.mitcr.clsexport.io.BinaryContainerWriter;
-import com.milaboratory.core.sequence.NucleotideSQPair;
-import com.milaboratory.core.sequence.SequenceQuality;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
 
 import java.io.DataInput;
 import java.io.DataOutput;
@@ -49,8 +49,8 @@
 
     @Override
     public Object read(DataInput input) throws IOException {
-        NucleotideSequenceImpl sequence = (NucleotideSequenceImpl) NucleotideSequenceIO.INSTANCE.read(input);
-        SequenceQuality quality = (SequenceQuality) SequenceQualityIO.INSTANCE.read(input);
+        NucleotideSequence sequence = (NucleotideSequence) NucleotideSequenceIO.INSTANCE.read(input);
+        SequenceQualityPhred quality = (SequenceQualityPhred) SequenceQualityIO.INSTANCE.read(input);
         return new NucleotideSQPair(sequence, quality);
     }
 
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSequenceIO.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSequenceIO.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSequenceIO.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/NucleotideSequenceIO.java	2013-10-09 08:03:10.000000000 +0000
@@ -20,10 +20,10 @@
  */
 package com.milaboratory.mitcr.clsexport.io.serializers;
 
+import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.mitcr.clsexport.io.BinaryContainerReader;
 import com.milaboratory.mitcr.clsexport.io.BinaryContainerWriter;
 import com.milaboratory.mitcr.clsexport.io.WrongStructureException;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
 import com.milaboratory.util.Bit2Array;
 
 import java.io.DataInput;
@@ -48,12 +48,12 @@
         if (s != 'S')
             throw new WrongStructureException();
         Bit2Array storage = Bit2ArrayIO.read(input);
-        return NucleotideSequenceImpl.fromStorage(storage);
+        return new NucleotideSequence(storage);
     }
 
     @Override
     public boolean canWrite(Object object) {
-        return object.getClass() == NucleotideSequenceImpl.class;
+        return object.getClass() == NucleotideSequence.class;
     }
 
     @Override
@@ -63,8 +63,8 @@
 
     @Override
     public void write(DataOutput output, Object object) throws IOException {
-        NucleotideSequenceImpl sequence = (NucleotideSequenceImpl) object;
+        NucleotideSequence sequence = (NucleotideSequence) object;
         output.writeByte('S');
-        Bit2ArrayIO.write(output, sequence.getInnerStorage());
+        Bit2ArrayIO.write(output, sequence.getInnerData());
     }
 }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/SequenceQualityIO.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/SequenceQualityIO.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/SequenceQualityIO.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/clsexport/io/serializers/SequenceQualityIO.java	2013-10-09 08:03:10.000000000 +0000
@@ -20,9 +20,9 @@
  */
 package com.milaboratory.mitcr.clsexport.io.serializers;
 
+import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 import com.milaboratory.mitcr.clsexport.io.BinaryContainerReader;
 import com.milaboratory.mitcr.clsexport.io.BinaryContainerWriter;
-import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 
 import java.io.DataInput;
 import java.io.DataOutput;
@@ -67,8 +67,8 @@
         if (object.getClass() == SequenceQualityPhred.class) {
             SequenceQualityPhred sq = (SequenceQualityPhred) object;
             output.writeByte(0);
-            output.writeInt(sq.getRawData().length);
-            output.write(sq.getRawData());
+            output.writeInt(sq.size());
+            output.write(sq.getInnerData());
         }
     }
 }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/pipeline/FullPipeline.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/pipeline/FullPipeline.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/pipeline/FullPipeline.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/pipeline/FullPipeline.java	2013-10-09 08:03:10.000000000 +0000
@@ -28,6 +28,7 @@
 import com.milaboratory.core.clone.CloneSet;
 import com.milaboratory.core.clone.CloneSetClustered;
 import com.milaboratory.core.segment.DefaultSegmentLibrary;
+import com.milaboratory.core.segment.SegmentGroupType;
 import com.milaboratory.core.segment.SegmentLibrary;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
@@ -146,6 +147,11 @@
                     parameters.getQualityInterpretationStrategy(), saveBackwardLinks, executorService,
                     listener == null ? null : listener.getCloneGeneratorListener());
 
+            //Initialization of CloneGenerator
+            generator.preInitialize(library.getGroup(parameters.getSpecies(), parameters.getGene(), SegmentGroupType.Variable),
+                    library.getGroup(parameters.getSpecies(), parameters.getGene(), SegmentGroupType.Joining),
+                    library.getGroup(parameters.getSpecies(), parameters.getGene(), SegmentGroupType.Diversity));
+
             //Setting progress reporter
             stage = "Individual sequence analysis & clone generation";
 
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/pipeline/Parameters.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/pipeline/Parameters.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/pipeline/Parameters.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/pipeline/Parameters.java	2013-10-09 08:03:10.000000000 +0000
@@ -23,6 +23,7 @@
 import com.milaboratory.core.segment.Gene;
 import com.milaboratory.core.segment.Species;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractorParameters;
+import com.milaboratory.mitcr.cli.BuildInformationProvider;
 import com.milaboratory.mitcr.clonegenerator.BasicCloneGeneratorParameters;
 import com.milaboratory.mitcr.clonegenerator.CloneGeneratorParameters;
 import com.milaboratory.mitcr.clonegenerator.CloneGeneratorParametersDeserializer;
@@ -39,6 +40,7 @@
  * @author Shugay Mikhail (mikhail.shugay@gmail.com)
  */
 public final class Parameters {
+    public static final String FORMAT_VERSION = "1.0";
     private Gene gene;
     private Species species;
     private QualityInterpretationStrategy qualityInterpretationStrategy = new DummyQualityInterpretationStrategy(); //Do not take quality information into account while processing sequences
@@ -88,6 +90,16 @@
     }
 
     public static Parameters fromXML(Element e) {
+        //Extracting format information
+        String format = e.getChildTextTrim("format");
+
+        if (format == null) //Backward compatibility
+            format = "1.0";
+
+        //Checking for compatibility
+        if (!format.equals(FORMAT_VERSION))
+            throw new RuntimeException("Unsupported parameters format version.");
+
         Element clusterizer = e.getChild("clusterizer");
         return new Parameters(Gene.fromXML(e.getChildTextTrim("gene")),
                 Species.valueOf(e.getChildTextTrim("species")),
@@ -103,6 +115,11 @@
     }
 
     public Element asXML(Element e) {
+        //Adding format information
+        e.addContent(new Element("format").setText(FORMAT_VERSION));
+        String version = BuildInformationProvider.getVersion();
+        if (version != null)
+            e.addContent(new Element("exportedByVersion").setText(version));
         e.addContent(new Element("gene").setText(gene.getXmlRepresentation()));
         e.addContent(new Element("species").setText(species.name()));
         e.addContent(qualityInterpretationStrategy.asXML(new Element("qualityInterpretationStrategy")));
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/qualitystrategy/IlluminaQualityInterpretationStrategy.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/qualitystrategy/IlluminaQualityInterpretationStrategy.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/qualitystrategy/IlluminaQualityInterpretationStrategy.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/qualitystrategy/IlluminaQualityInterpretationStrategy.java	2013-10-09 08:03:10.000000000 +0000
@@ -97,7 +97,7 @@
 
                     @Override
                     public boolean isBad(int position) {
-                        return nucleotideSQPair.getQuality().rawQualityValue(position) < threshold;
+                        return nucleotideSQPair.getQuality().value(position) < threshold;
                     }
                 };
             }
@@ -121,7 +121,7 @@
 
                     @Override
                     public boolean isBad(int position) {
-                        return read.getData().getQuality().rawQualityValue(position) < threshold;
+                        return read.getData().getQuality().value(position) < threshold;
                     }
                 };
             }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapper.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapper.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapper.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapper.java	2013-10-09 08:03:10.000000000 +0000
@@ -24,7 +24,6 @@
 import com.milaboratory.core.segment.SegmentGroupContainer;
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.core.sequence.util.NucleotideRCSequence;
 import com.milaboratory.util.BitArray;
 
 import java.util.ArrayList;
@@ -51,7 +50,7 @@
             wrappers.add(new SegmentSequenceWrapper(al.getSequence(), al));
             if (searchRC)
                 wrappers.add(new SegmentSequenceWrapper(
-                        new NucleotideRCSequence(al.getSequence()), al));
+                        al.getSequence().getReverseComplement(), al));
         }
         this.wrappers = wrappers.toArray(new SegmentSequenceWrapper[wrappers.size()]);
     }
diff -Nru mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/vdjmapping/VDJSegmentsMapper.java mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/vdjmapping/VDJSegmentsMapper.java
--- mitcr-1.0.2/src/main/java/com/milaboratory/mitcr/vdjmapping/VDJSegmentsMapper.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/main/java/com/milaboratory/mitcr/vdjmapping/VDJSegmentsMapper.java	2013-10-09 08:03:10.000000000 +0000
@@ -21,7 +21,6 @@
 package com.milaboratory.mitcr.vdjmapping;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
-import com.milaboratory.core.sequence.util.NucleotideSubSequence;
 
 /**
  * A joint mapper for V, J and D(optional)  segments.
@@ -81,8 +80,7 @@
                 int to = results[1].getSegmentBorderFrom() - 1;
                 if (from < to) {
                     //search for d gene between v end and j start
-                    NucleotideSubSequence subSequence = new NucleotideSubSequence(wrapper.getSequence(), from, to - from + 1);
-                    dResult = dMapper.map(subSequence);
+                    dResult = dMapper.map(wrapper.getSequence().getRange(from, to + 1));
                     if (dResult != null) {
                         dResult.segmentBorderFrom += from;
                         dResult.segmentBorderTo += from;
diff -Nru mitcr-1.0.2/src/scripts/mitcr mitcr-1.0.3/src/scripts/mitcr
--- mitcr-1.0.2/src/scripts/mitcr	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/scripts/mitcr	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+freem=`free -m | sed 's/\s\+/ /g' | cut -d' ' -f4 | head -n 2 | tail -n 1 | tr -d '\n'`
+buffersm=`free -m | sed 's/\s\+/ /g' | cut -d' ' -f6 | head -n 2 | tail -n 1 | tr -d '\n'`
+cachedm=`free -m | sed 's/\s\+/ /g' | cut -d' ' -f7 | head -n 2 | tail -n 1 | tr -d '\n'`
+
+free_memory=`echo "$freem+$buffersm+$cachedm" | bc`
+
+java_memory=`echo "$free_memory*9/10" | bc`
+
+classpath="/usr/share/java/micommons.jar:/usr/share/java/redberry-pipe.jar:/usr/share/java/jdom1.jar:/usr/share/java/commons-compress.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-cli.jar:/usr/share/java/trove3.jar:/usr/share/java/mitcr.jar"
+xmx="${java_memory}m"
+params=("$@")
+
+java_path=`ls -1 /usr/lib/jvm | grep java-7-openjdk | grep -v common | tr -d '\n'`
+if [ -z "$java_path" ]; then
+    java_path=`ls -1 /usr/lib/jvm | grep java-7 | head -n 1 | tr -d '\n'`
+fi
+java_path="/usr/lib/jvm/${java_path}/bin/java"
+
+if [ ! -f "$java_path" ]; then
+    echo "Can't find Java 7 on your system."
+fi
+
+auto_memory=true
+
+for ((n=0; n < ${#params[@]}; n++))
+do
+    if [[ "${params[$n]}" == -Xmx* ]]
+    then
+	xmx="${params[$n]:4}"
+	unset params[$n]
+	auto_memory=false
+    fi
+done
+
+if $auto_memory ; then
+    echo "Max java heap space automatically set to ${xmx} (90% of free memory). Use '-Xmx' option to adjust this value."
+else
+    echo "Java heap space set to ${xmx}."
+fi
+
+options="-XX:+AggressiveOpts"
+
+if [[ `uname -i` == "x86_64" ]]; then
+    options="$options -XX:+DoEscapeAnalysis"
+fi
+
+eval "${java_path} -Dexecutable=mitcr $options -cp $classpath -Xmx${xmx} com.milaboratory.mitcr.cli.Main ${params[@]}"
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/core/io/CloneSetIOTest.java mitcr-1.0.3/src/test/java/com/milaboratory/core/io/CloneSetIOTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/core/io/CloneSetIOTest.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/core/io/CloneSetIOTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,62 @@
+/*
+ * MiTCR <http://milaboratory.com>
+ *
+ * Copyright (c) 2010-2013:
+ *     Bolotin Dmitriy     <bolotin.dmitriy@gmail.com>
+ *     Chudakov Dmitriy    <chudakovdm@mail.ru>
+ *
+ * MiTCR is free software: you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+package com.milaboratory.core.io;
+
+import com.milaboratory.core.clone.Clone;
+import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.mitcr.cli.ExportDetalizationLevel;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.io.PrintStream;
+import java.util.HashSet;
+import java.util.zip.GZIPInputStream;
+
+import static com.milaboratory.core.io.CloneSetIO.exportCloneSet;
+import static com.milaboratory.core.io.CloneSetIO.importCloneSet;
+
+public class CloneSetIOTest {
+    @Test
+    public void testExportImport() throws Exception {
+        //Reading test cloneSet
+        InputStream stream = this.getClass().getClassLoader().getResourceAsStream("test_cloneSet.txt.gz");
+        GZIPInputStream unzippedStream = new GZIPInputStream(stream);
+        CloneSet cloneSet = importCloneSet(unzippedStream);
+        unzippedStream.close();
+
+        //Creating set of clones
+        HashSet<Clone> clones = new HashSet<>(cloneSet.getClones());
+
+        //Writing and then reading the clone set
+        final ByteArrayOutputStream os = new ByteArrayOutputStream();
+        exportCloneSet(new PrintStream(os), cloneSet, ExportDetalizationLevel.Full);
+        final byte[] result = os.toByteArray();
+        final ByteArrayInputStream is = new ByteArrayInputStream(result);
+        final CloneSet testCloneSet = importCloneSet(is);
+
+        //Testing that deserialization result is the same as serialization
+        Assert.assertEquals(cloneSet.getTotalCount(), testCloneSet.getTotalCount());
+        Assert.assertTrue(clones.containsAll(testCloneSet.getClones()));
+    }
+}
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/core/util/CloneSetsComparatorTest.java mitcr-1.0.3/src/test/java/com/milaboratory/core/util/CloneSetsComparatorTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/core/util/CloneSetsComparatorTest.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/core/util/CloneSetsComparatorTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,29 @@
+package com.milaboratory.core.util;
+
+import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.core.io.CloneSetIO;
+import com.milaboratory.util.CompressionType;
+import junit.framework.Assert;
+import org.junit.Test;
+
+public class CloneSetsComparatorTest {
+    private CloneSet loadCloneSet(String fileName) throws Exception {
+        return CloneSetIO.importCloneSet(
+                this.getClass().getClassLoader().
+                        getResourceAsStream(fileName), CompressionType.GZIP);
+    }
+
+    @Test
+    public void test1() throws Exception {
+        CloneSet cloneSetFlex1 = loadCloneSet("o_good_flex1.txt.gz"),
+                cloneSetFlex2 = loadCloneSet("o_good_flex2.txt.gz"),
+                cloneSetJPrimer1 = loadCloneSet("o_good_jprimer1.txt.gz"),
+                cloneSetJPrimer2 = loadCloneSet("o_good_jprimer2.txt.gz");
+
+        Assert.assertEquals(0.0, CloneSetsComparator.compare(cloneSetFlex1, cloneSetFlex2).difference, 1E-10);
+        Assert.assertEquals(0.0, CloneSetsComparator.compare(cloneSetJPrimer1, cloneSetJPrimer2).difference, 1E-10);
+
+        //Commutativity test
+        Assert.assertEquals(CloneSetsComparator.compare(cloneSetJPrimer2, cloneSetFlex1).difference, CloneSetsComparator.compare(cloneSetFlex1, cloneSetJPrimer2).difference, 1E-10);
+    }
+}
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/MiTCRTestUtils.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/MiTCRTestUtils.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/MiTCRTestUtils.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/MiTCRTestUtils.java	2013-10-09 08:03:10.000000000 +0000
@@ -20,9 +20,9 @@
  */
 package com.milaboratory.mitcr;
 
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.SSequencingDataReader;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractorParameters;
 import com.milaboratory.mitcr.cdrextraction.Strand;
 import com.milaboratory.mitcr.vdjmapping.AlignmentDirection;
@@ -40,7 +40,7 @@
     public static SSequencingDataReader getSampleTReader() {
         try {
             return new SFastqReader(MiTCRTestUtils.class.getClassLoader().getSystemResourceAsStream("good_ds_test.fastq.gz"),
-                    QualityStringFormat.Illumina18, CompressionType.GZIP);
+                    QualityFormat.Phred33, CompressionType.GZIP);
         } catch (IOException ex) {
             throw new RuntimeException(ex);
         }
@@ -52,7 +52,7 @@
     public static SSequencingDataReader getSampleFReader() {
         try {
             return new SFastqReader(MiTCRTestUtils.class.getClassLoader().getSystemResourceAsStream("cdr3_sample.fastq.gz"),
-                    QualityStringFormat.Illumina18, CompressionType.GZIP);
+                    QualityFormat.Phred33, CompressionType.GZIP);
         } catch (IOException ex) {
             throw new RuntimeException(ex);
         }
@@ -69,6 +69,6 @@
     }
 
     public static SSequencingDataReader getReaderFromString(String readsContent) throws IOException {
-        return new SFastqReader(new ByteArrayInputStream(readsContent.getBytes()), QualityStringFormat.Illumina18, CompressionType.None);
+        return new SFastqReader(new ByteArrayInputStream(readsContent.getBytes()), QualityFormat.Phred33, CompressionType.None);
     }
 }
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorFactoryTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorFactoryTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorFactoryTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorFactoryTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -29,10 +29,9 @@
 import com.milaboratory.core.sequence.aminoacid.AminoAcidAlphabet;
 import com.milaboratory.core.sequence.aminoacid.CDRAminoAcidSequence;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.SSequencingDataReader;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.pipeline.ParameterPresets;
 import com.milaboratory.mitcr.qualitystrategy.DummyQualityInterpretationStrategy;
@@ -51,7 +50,7 @@
     @Test
     public void testEmptyBarcode() throws Exception {
         String sequenceString = "TTTTGATTGCTGGCACAGAAGTACACAGATGTCTGGGAGGGAGCAGCCGACTCCAGCCTGAGCGAGAACTCC";
-        NucleotideSequence sequence = NucleotideSequenceImpl.fromSequence(sequenceString);
+        NucleotideSequence sequence = new NucleotideSequence(sequenceString);
         NucleotideSQPair pair = new NucleotideSQPair(sequence);
         CDR3ExtractorFromSQPair extractor = new CDR3ExtractorFromSQPair(Species.HomoSapiens, Gene.TRB, ParameterPresets.getFlex().getCDR3ExtractorParameters(),
                 DefaultSegmentLibrary.load(), new DummyQualityInterpretationStrategy());
@@ -65,7 +64,7 @@
     public void testExactMatch() throws URISyntaxException, IOException, InterruptedException {
         SSequencingDataReader reads =
                 new SFastqReader(ClassLoader.getSystemResourceAsStream("cdr3_sample.fastq.gz"),
-                        QualityStringFormat.Illumina18, CompressionType.GZIP);
+                        QualityFormat.Phred33, CompressionType.GZIP);
 
         CDR3ExtractorFactory<SSequencingRead> extractorFactory = new CDR3ExtractorFactoryFromSRead(Species.HomoSapiens, Gene.TRB,
                 getFlexCDR3ExtractionParameters(), library,
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cdrextraction/CDR3ExtractorTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -28,9 +28,9 @@
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.aminoacid.AminoAcidAlphabet;
 import com.milaboratory.core.sequence.aminoacid.CDRAminoAcidSequence;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.SSequencingDataReader;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.qualitystrategy.DummyQualityInterpretationStrategy;
 import com.milaboratory.mitcr.qualitystrategy.IlluminaQualityInterpretationStrategy;
@@ -80,7 +80,7 @@
     @Test
     public void testIllumina() throws URISyntaxException, IOException, InterruptedException {
         File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Phred33, CompressionType.GZIP);
 
         CDR3Extractor<SSequencingRead> extractor;
         extractor = new CDR3ExtractorFromSRead(Species.HomoSapiens, Gene.TRB,
@@ -111,7 +111,7 @@
     @Test
     public void testDifference() throws Exception {
         File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Phred33, CompressionType.GZIP);
 
         CDR3Extractor<SSequencingRead> extractor = new CDR3ExtractorFromSRead(Species.HomoSapiens, Gene.TRB,
                 getFlexCDR3ExtractionParameters(), library,
@@ -134,7 +134,7 @@
 
         int count = 0;
 
-        //SFastqWriter writer = new SFastqWriter(System.out, QualityStringFormat.Illumina18, CompressionType.None);
+        //SFastqWriter writer = new SFastqWriter(System.out, QualityFormat.Illumina18, CompressionType.None);
 
         while ((result = results.take()) != null) {
             if (result.getCDR3() == null)
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cli/ParametersIOTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cli/ParametersIOTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cli/ParametersIOTest.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cli/ParametersIOTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,21 @@
+package com.milaboratory.mitcr.cli;
+
+import com.milaboratory.mitcr.pipeline.ParameterPresets;
+import com.milaboratory.mitcr.pipeline.Parameters;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class ParametersIOTest {
+    @Test
+    public void test1() throws Exception {
+        Parameters params = ParameterPresets.
+                getFlex();
+        String paramsString = ParametersIO.
+                exportParametersToString(params);
+        Assert.assertEquals(-1,
+                paramsString.indexOf('\n'));
+        Assert.assertEquals(params,
+                ParametersIO.importParametersFromString(paramsString));
+
+    }
+}
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cli/TabDelimitedImporterTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cli/TabDelimitedImporterTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/cli/TabDelimitedImporterTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/cli/TabDelimitedImporterTest.java	1970-01-01 00:00:00.000000000 +0000
@@ -1,58 +0,0 @@
-/*
- * MiTCR <http://milaboratory.com>
- *
- * Copyright (c) 2010-2013:
- *     Bolotin Dmitriy     <bolotin.dmitriy@gmail.com>
- *     Chudakov Dmitriy    <chudakovdm@mail.ru>
- *
- * MiTCR is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option)
- * any later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
- * more details.
- *
- * You should have received a copy of the GNU General Public License along
- * with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-package com.milaboratory.mitcr.cli;
-
-import com.milaboratory.core.clone.Clone;
-import com.milaboratory.core.clone.CloneSet;
-import org.junit.Assert;
-import org.junit.Test;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.InputStream;
-import java.io.PrintStream;
-import java.util.HashSet;
-import java.util.zip.GZIPInputStream;
-
-public class TabDelimitedImporterTest {
-    @Test
-    public void testExportImport() throws Exception {
-        //Reading test cloneSet
-        InputStream stream = this.getClass().getClassLoader().getResourceAsStream("test_cloneSet.txt.gz");
-        GZIPInputStream unzippedStream = new GZIPInputStream(stream);
-        CloneSet cloneSet = TabDelimitedImporter.importCloneSet(unzippedStream);
-        unzippedStream.close();
-
-        //Creating set of clones
-        HashSet<Clone> clones = new HashSet<>(cloneSet.getClones());
-
-        //Writing and then reading the clone set
-        final ByteArrayOutputStream os = new ByteArrayOutputStream();
-        TabDelimitedExporter.exportCloneSet(new PrintStream(os), cloneSet, ExportDetalizationLevel.Full);
-        final byte[] result = os.toByteArray();
-        final ByteArrayInputStream is = new ByteArrayInputStream(result);
-        final CloneSet testCloneSet = TabDelimitedImporter.importCloneSet(is);
-
-        //Testing that deserialization result is the same as serialization
-        Assert.assertEquals(cloneSet.getTotalCount(), testCloneSet.getTotalCount());
-        Assert.assertTrue(clones.containsAll(testCloneSet.getClones()));
-    }
-}
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculatorTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculatorTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculatorTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clonegenerator/AverageQualityCalculatorTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -8,7 +8,7 @@
 public class AverageQualityCalculatorTest {
     @Test
     public void test1() throws Exception {
-        RandomGenerator rg = new MersenneTwister();
+        RandomGenerator rg = new MersenneTwister(234562);
 
         SummaryStatistics ss = new SummaryStatistics();
         byte accumulator = 0;
@@ -27,8 +27,8 @@
 
     @Test
     public void test2() throws Exception {
-        RandomGenerator rg = new Well19937a();
-        RandomData rdg = new RandomDataImpl(new Well44497a());
+        RandomGenerator rg = new Well19937a(223441);
+        RandomData rdg = new RandomDataImpl(new Well44497a(454213));
 
         final int sampleSize = 2000;
 
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGeneratorTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGeneratorTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGeneratorTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clonegenerator/BasicCloneGeneratorTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -27,9 +27,9 @@
 import com.milaboratory.core.segment.Gene;
 import com.milaboratory.core.segment.SegmentGroupType;
 import com.milaboratory.core.segment.Species;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.SSequencingDataReader;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSRead;
@@ -50,7 +50,7 @@
     @Test
     public void testExactMatch() throws URISyntaxException, IOException, InterruptedException {
         File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Phred33, CompressionType.GZIP);
 
         TestCGListener listener = new TestCGListener();
 
@@ -121,7 +121,7 @@
 
     private CloneSet getCloneSet(AccumulatorCloneFactory factory) throws URISyntaxException, IOException, InterruptedException {
         File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Phred33, CompressionType.GZIP);
 
         TestCGListener listener = new TestCGListener();
 
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/LQMappingCloneGeneratorTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clonegenerator/LQMappingCloneGeneratorTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clonegenerator/LQMappingCloneGeneratorTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clonegenerator/LQMappingCloneGeneratorTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -26,9 +26,9 @@
 import com.milaboratory.core.clone.CloneSet;
 import com.milaboratory.core.segment.Gene;
 import com.milaboratory.core.segment.Species;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.SSequencingDataReader;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSRead;
@@ -62,7 +62,7 @@
     @Test
     public void test0() throws InterruptedException, IOException, URISyntaxException {
         File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Phred33, CompressionType.GZIP);
 
         CDR3ExtractorFromSRead extractor = new CDR3ExtractorFromSRead(Species.HomoSapiens, Gene.TRB,
                 getFlexCDR3ExtractionParameters(), library,
@@ -156,7 +156,7 @@
     @Test
     public void testProportional() throws Exception {
         //File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        //SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        //SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Illumina18, CompressionType.GZIP);
         //        |           |
         //TGCAGCGCACACATGAACACAGAAGCTTTCTTT - clone 1
         //TGCAGCGCTCACATGAACACTGAAGCTTTCTTT - clone 2
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clusterization/PenaltyBasedFastClusterizerTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clusterization/PenaltyBasedFastClusterizerTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/clusterization/PenaltyBasedFastClusterizerTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/clusterization/PenaltyBasedFastClusterizerTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -31,7 +31,7 @@
 import com.milaboratory.core.sequence.util.SequencesUtils;
 import com.milaboratory.core.sequencing.io.SSequencingDataReader;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult;
 import com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSRead;
@@ -57,7 +57,7 @@
     @Test
     public void firstTest() throws InterruptedException, URISyntaxException, IOException {
         File sample = new File(ClassLoader.getSystemResource("cdr3_sample.fastq.gz").toURI());
-        SSequencingDataReader reader = new SFastqReader(sample, QualityStringFormat.Illumina18, CompressionType.GZIP);
+        SSequencingDataReader reader = new SFastqReader(sample, QualityFormat.Phred33, CompressionType.GZIP);
 
         CDR3ExtractorFromSRead extractor = new CDR3ExtractorFromSRead(Species.HomoSapiens, Gene.TRB,
                 getFlexCDR3ExtractionParameters(), library,
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/pipeline/FullPipelineTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/pipeline/FullPipelineTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/pipeline/FullPipelineTest.java	1970-01-01 00:00:00.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/pipeline/FullPipelineTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -0,0 +1,35 @@
+package com.milaboratory.mitcr.pipeline;
+
+import com.milaboratory.core.clone.CloneSet;
+import com.milaboratory.core.io.CloneSetIO;
+import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
+import com.milaboratory.core.util.CloneSetsComparator;
+import com.milaboratory.util.CompressionType;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class FullPipelineTest {
+    private CloneSet loadCloneSet(String fileName) throws Exception {
+        return CloneSetIO.importCloneSet(
+                this.getClass().getClassLoader().
+                        getResourceAsStream(fileName), CompressionType.GZIP);
+    }
+
+    private void test(Parameters params, String referenceName) throws Exception {
+        FullPipeline pipeline = new FullPipeline(new SFastqReader(this.getClass().getClassLoader().
+                getResourceAsStream("good_ds_test.fastq.gz"), CompressionType.GZIP), params);
+        pipeline.run();
+        CloneSet csResult = pipeline.getResult();
+        Assert.assertEquals(0.0, CloneSetsComparator.compare(csResult, loadCloneSet(referenceName)).difference, 0.005);
+    }
+
+    @Test
+    public void testFlex1() throws Exception {
+        test(ParameterPresets.getFlex(), "o_good_flex1.txt.gz");
+    }
+
+    @Test
+    public void testJPrimer1() throws Exception {
+        test(ParameterPresets.getJPrimer(), "o_good_jprimer1.txt.gz");
+    }
+}
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/AbstractMapperTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/AbstractMapperTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/AbstractMapperTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/AbstractMapperTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -22,7 +22,7 @@
 
 import com.milaboratory.core.segment.SegmentLibrary;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat;
+import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.util.CompressionType;
 import org.junit.BeforeClass;
@@ -81,7 +81,7 @@
         library = SegmentLibrary.readFromFile(segmentsFile);
 
         SFastqReader reader = new SFastqReader(new ByteArrayInputStream(readsForTest.getBytes()),
-                QualityStringFormat.Illumina18, CompressionType.None);
+                QualityFormat.Phred33, CompressionType.None);
 
         SSequencingRead read;
         List<SSequencingRead> readsList = new ArrayList<>();
@@ -99,13 +99,13 @@
 
     /*private static SequenceWrapper getWrapper(String fileName, boolean mark) {
         try {
-            FASTQReaderOld reader = new FASTQReaderOld(fileName, QualityStringFormat.Illumina15);
+            FASTQReaderOld reader = new FASTQReaderOld(fileName, QualityFormat.Illumina15);
             NucleotideSQPair pair = reader.next().getData();
             BitArray ba = new BitArray(pair.size());
             ba.clearAll();
             if (mark)
                 for (int i = 0; i < pair.size(); ++i)
-                    if (pair.getQuality().rawQualityValue(i) < 10)
+                    if (pair.getQuality().value(i) < 10)
                         ba.set(i);
             SequenceWrapper wrapper = new SequenceWrapper(ba, pair);
             reader.close();
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapperTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapperTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapperTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/DSegmentMapperTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -5,8 +5,6 @@
 import com.milaboratory.core.segment.SegmentGroupType;
 import com.milaboratory.core.segment.Species;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
-import com.milaboratory.core.sequence.util.NucleotideRCSequence;
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;
@@ -16,8 +14,8 @@
     public void testGeneral() throws Exception {
         String seq0str = "TGCAGCGTACCGGGGGGCTCAAATGAAAAACTGTTTTTT";
 
-        NucleotideSequence seq0 = NucleotideSequenceImpl.fromSequence(seq0str);
-        NucleotideSequence seq0rc = new NucleotideRCSequence(seq0);
+        NucleotideSequence seq0 = new NucleotideSequence(seq0str);
+        NucleotideSequence seq0rc = seq0.getReverseComplement();
 
         DSegmentMapper mapperT = new DSegmentMapper(DefaultSegmentLibrary.load().getGroup(Species.HomoSapiens, Gene.TRB, SegmentGroupType.Diversity), 5, true);
         DSegmentMapper mapperF = new DSegmentMapper(DefaultSegmentLibrary.load().getGroup(Species.HomoSapiens, Gene.TRB, SegmentGroupType.Diversity), 5, false);
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/SimplestAlignmentTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/SimplestAlignmentTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/SimplestAlignmentTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/SimplestAlignmentTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -1,7 +1,6 @@
 package com.milaboratory.mitcr.vdjmapping;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;
@@ -10,8 +9,8 @@
 public class SimplestAlignmentTest {
     @Test
     public void test1() throws Exception {
-        NucleotideSequence target = NucleotideSequenceImpl.fromSequence("ATTAGACA"),
-                query = NucleotideSequenceImpl.fromSequence("ATTAGACA");
+        NucleotideSequence target = new NucleotideSequence("ATTAGACA"),
+                query = new NucleotideSequence("ATTAGACA");
         SimplestAlignment alignment = SimplestAlignment.build(target, query, 3);
         assertEquals(target.size(), alignment.length);
         assertEquals(0, alignment.targetFrom);
@@ -20,8 +19,8 @@
 
     @Test
     public void test2() throws Exception {
-        NucleotideSequence target = NucleotideSequenceImpl.fromSequence("ATTAGACA"),
-                query = NucleotideSequenceImpl.fromSequence("ATTGGACA");
+        NucleotideSequence target = new NucleotideSequence("ATTAGACA"),
+                query = new NucleotideSequence("ATTGGACA");
         SimplestAlignment alignment = SimplestAlignment.build(target, query, 3);
         assertEquals(4, alignment.length);
         assertEquals(4, alignment.targetFrom);
@@ -30,8 +29,8 @@
 
     @Test
     public void test3() throws Exception {
-        NucleotideSequence target = NucleotideSequenceImpl.fromSequence("ACA"),
-                query = NucleotideSequenceImpl.fromSequence("ATTGGACA");
+        NucleotideSequence target = new NucleotideSequence("ACA"),
+                query = new NucleotideSequence("ATTGGACA");
         SimplestAlignment alignment = SimplestAlignment.build(target, query, 3);
         assertEquals(3, alignment.length);
         assertEquals(0, alignment.targetFrom);
@@ -40,16 +39,16 @@
 
     @Test
     public void test4() throws Exception {
-        NucleotideSequence target = NucleotideSequenceImpl.fromSequence("ACA"),
-                query = NucleotideSequenceImpl.fromSequence("ATTGGACA");
+        NucleotideSequence target = new NucleotideSequence("ACA"),
+                query = new NucleotideSequence("ATTGGACA");
         SimplestAlignment alignment = SimplestAlignment.build(target, query, 4);
         assertNull(alignment);
     }
 
     @Test
     public void test5() throws Exception {
-        NucleotideSequence target = NucleotideSequenceImpl.fromSequence("ATTAGACA"),
-                query = NucleotideSequenceImpl.fromSequence("AGTGGAGA");
+        NucleotideSequence target = new NucleotideSequence("ATTAGACA"),
+                query = new NucleotideSequence("AGTGGAGA");
         SimplestAlignment alignment = SimplestAlignment.build(target, query, 3);
         assertEquals(3, alignment.length);
         assertEquals(3, alignment.targetFrom);
@@ -58,8 +57,8 @@
 
     @Test
     public void test6() throws Exception {
-        NucleotideSequence target = NucleotideSequenceImpl.fromSequence("ATTAGACA"),
-                query = NucleotideSequenceImpl.fromSequence("AGAC");
+        NucleotideSequence target = new NucleotideSequence("ATTAGACA"),
+                query = new NucleotideSequence("AGAC");
         SimplestAlignment alignment = SimplestAlignment.build(target, query, 3);
         assertEquals(4, alignment.length);
         assertEquals(3, alignment.targetFrom);
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/tree/UniDirectionSegmentMapperTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/tree/UniDirectionSegmentMapperTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/tree/UniDirectionSegmentMapperTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/tree/UniDirectionSegmentMapperTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -24,7 +24,6 @@
 package com.milaboratory.mitcr.vdjmapping.tree;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.core.sequence.util.NucleotideSubSequence;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.mitcr.qualitystrategy.IlluminaQualityInterpretationStrategy;
 import com.milaboratory.mitcr.vdjmapping.*;
@@ -41,7 +40,7 @@
         VJSegmentMapper<SSequencingRead> mapper = VJSegmentMapperFactory.createMapperForSReads(container, params, new IlluminaQualityInterpretationStrategy((byte) 20));
         VJSegmentMappingResult result = mapper.map(reads[3]);
         String assertSequence = "TTCTACATCTGCAGT";
-        NucleotideSequence c = new NucleotideSubSequence(reads[3].getData().getSequence(), result.getRefPoint() - 12, 15);
+        NucleotideSequence c = reads[3].getData().getSequence().getRange(result.getRefPoint() - 12, result.getRefPoint() + 3);
         Assert.assertEquals(assertSequence, c.toString());
     }
 
@@ -51,7 +50,7 @@
         VJSegmentMapper<SSequencingRead> mapper = VJSegmentMapperFactory.createMapperForSReads(container, params, new IlluminaQualityInterpretationStrategy((byte) 20));
         VJSegmentMappingResult result = mapper.map(reads[3]);
         String assertSequence = "GTGCCCATCCTGAAGACAGCAGCTTCTACATCTGCAGT";
-        NucleotideSequence c = new NucleotideSubSequence(reads[3].getData().getSequence(), result.getRefPoint() - 35, 38);
+        NucleotideSequence c = reads[3].getData().getSequence().getRange(result.getRefPoint() - 35, result.getRefPoint() + 3);
         Assert.assertEquals(assertSequence, c.toString());
     }
 
diff -Nru mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/trivial/TrivialSegmentMapperTest.java mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/trivial/TrivialSegmentMapperTest.java
--- mitcr-1.0.2/src/test/java/com/milaboratory/mitcr/vdjmapping/trivial/TrivialSegmentMapperTest.java	2013-08-12 11:19:38.000000000 +0000
+++ mitcr-1.0.3/src/test/java/com/milaboratory/mitcr/vdjmapping/trivial/TrivialSegmentMapperTest.java	2013-10-09 08:03:10.000000000 +0000
@@ -24,7 +24,7 @@
 import com.milaboratory.core.segment.SegmentGroupContainer;
 import com.milaboratory.core.segment.Species;
 import com.milaboratory.core.sequence.NucleotideSQPair;
-import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl;
+import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.mitcr.pipeline.ParameterPresets;
 import com.milaboratory.mitcr.pipeline.Parameters;
 import com.milaboratory.mitcr.qualitystrategy.DummyQualityInterpretationStrategy;
@@ -44,7 +44,7 @@
     @Test
     public void testFirst() throws Exception {
         NucleotideSQPair testSequence = new NucleotideSQPair(
-                NucleotideSequenceImpl.fromSequence("TCTGAGTCAACAGTCTCCAGAATAAGGACGGAGCATTTTCCCCTGACCCTGGAG" +
+                new NucleotideSequence("TCTGAGTCAACAGTCTCCAGAATAAGGACGGAGCATTTTCCCCTGACCCTGGAG" +
                         //                                TGTGCCAGCAGCGAGAGACAGGGGACGCAGTATTTT
                         "TCTGCCAGGCCCTCACATACCTCTCAGTCCCTCTGTGCCAGCAGCGAGAGACAGGGGACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTC"));
 
@@ -69,7 +69,7 @@
                 //                                                               VVVVVVVVVVVVV.............................
                 //                          GGAGTTGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGT       -  TRBV6-6*02
                 //                          GCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTactc  -  TRBV6-5*01
-                NucleotideSequenceImpl.fromSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCCCTAGCGGGAGAGCACGAGCAGTACTTC"));
+                new NucleotideSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCCCTAGCGGGAGAGCACGAGCAGTACTTC"));
 
         IlluminaQualityInterpretationStrategy ill = new IlluminaQualityInterpretationStrategy((byte) 25);
         VJSegmentMappingResult resultVJ;
@@ -94,7 +94,7 @@
                 //                                                               VVVVVVVVVVVVV.............................
                 //                          GGAGTTGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGT       -  TRBV6-6*02
                 //                          GCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTactc  -  TRBV6-5*01
-                NucleotideSequenceImpl.fromSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGAAGTTCCCTAGCGGGAGAGCACGAGCAGTACTTC"));
+                new NucleotideSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGAAGTTCCCTAGCGGGAGAGCACGAGCAGTACTTC"));
 
         IlluminaQualityInterpretationStrategy ill = new IlluminaQualityInterpretationStrategy((byte) 25);
         VJSegmentMappingResult resultVJ;
@@ -119,7 +119,7 @@
                 //                                                               VVVVVVVVVVVVV.............................
                 //                          GGAGTTGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGT       -  TRBV6-6*02
                 //                          GCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTactc  -  TRBV6-5*01
-                NucleotideSequenceImpl.fromSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCACTTCCCTAGCGGGAGAGCACGAGCAGTACTTC"));
+                new NucleotideSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCACTTCCCTAGCGGGAGAGCACGAGCAGTACTTC"));
 
         IlluminaQualityInterpretationStrategy ill = new IlluminaQualityInterpretationStrategy((byte) 25);
         VJSegmentMappingResult resultVJ;
@@ -146,19 +146,19 @@
                 //                                                               VVVVVVVVVVVVV.............................
                 //                          GGAGTTGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGT       -
                 //                          GCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTactc  -  TRBV6-5*01
-                NucleotideSequenceImpl.fromSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
+                new NucleotideSequence("TGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
                 vCDR3Chimera1 = new NucleotideSQPair(
                         //                                   ??????????                            VVVVVVVVVVVV..............................
-                        NucleotideSequenceImpl.fromSequence("GTACTTCTGTTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
+                        new NucleotideSequence("GTACTTCTGTTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
                 vCDR3Chimera2 = new NucleotideSQPair(
                         //                                   ????????????                            VVVVVVVVVVVV..............................
-                        NucleotideSequenceImpl.fromSequence("TGTGCCAGCAGTTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
+                        new NucleotideSequence("TGTGCCAGCAGTTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
                 vCDR3Chimera3 = new NucleotideSQPair(
                         //                                   ???????????????????                            VVVVVVVVVVVV..............................
-                        NucleotideSequenceImpl.fromSequence("TGTGTACTTCTGTGCCAGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
+                        new NucleotideSequence("TGTGTACTTCTGTGCCAGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC")),
                 vCDR3Chimera4 = new NucleotideSQPair(
                         //                                   ???????????????????             *         *    VVVVVVVVVVVV..............................
-                        NucleotideSequenceImpl.fromSequence("TGTGTACTTCTGTGCCAGCTGCTCCCTCCCAGTCATCTGTGTTCTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC"));
+                        new NucleotideSequence("TGTGTACTTCTGTGCCAGCTGCTCCCTCCCAGTCATCTGTGTTCTTCTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTC"));
 
 
         IlluminaQualityInterpretationStrategy ill = new IlluminaQualityInterpretationStrategy((byte) 25);
@@ -200,7 +200,7 @@
         TrivialSegmentMapper mapper = new TrivialSegmentMapper(container,
                 -1, 4, 12, 2, AlignmentDirection.Both);
 
-        NucleotideSQPair sequence = new NucleotideSQPair(NucleotideSequenceImpl.fromSequence(seqInt));
+        NucleotideSQPair sequence = new NucleotideSQPair(new NucleotideSequence(seqInt));
 
         VJSegmentMappingResult resultVJ;
 
@@ -220,24 +220,24 @@
                 //                                   |0        |10       |20       |30       |40       |50       |60
                 //                                   ............................JJJJJJJJJJJJJJJ
                 //                                                          CTCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG  -  TRBJ2-7*01
-                NucleotideSequenceImpl.fromSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
+                new NucleotideSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
                 jCDR3Chimera1 = new NucleotideSQPair(
                         //                                   |0        |10       |20       |30       |40       |50       |60       |70       |80
                         //                                                     ...........................JJJJJJJJJJJJJJJ
-                        NucleotideSequenceImpl.fromSequence("CCAGGCTCACGGTCACAGTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
+                        new NucleotideSequence("CCAGGCTCACGGTCACAGTGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
                 jCDR3MM1 = new NucleotideSQPair(
                         //                                   |0        |10       |20       |30       |40       |50       |60
                         //                                   ...........................JJJ*JJJJJJJJJJJ
-                        NucleotideSequenceImpl.fromSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACAAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
+                        new NucleotideSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACAAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
                 jCDR3MM2 = new NucleotideSQPair(
                         //                                   ...........................JJJ*JJJJJJ*JJJJ
-                        NucleotideSequenceImpl.fromSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTGCTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
+                        new NucleotideSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTGCTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
                 jCDR3MM3 = new NucleotideSQPair(
                         //                                   ...........................JJJ*JJJJJJJJJJJ
-                        NucleotideSequenceImpl.fromSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGGAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
+                        new NucleotideSequence("TGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGGAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG")),
                 jCDR3Chimera4 = new NucleotideSQPair(
                         //                                   ??????????????????...........................JJJJJJJJJJJJJJJ
-                        NucleotideSequenceImpl.fromSequence("CTTCGGGCCGGGCGCCAATGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTCGGG"));
+                        new NucleotideSequence("CTTCGGGCCGGGCGCCAATGTGCCAGCAGTTCTCTAGCGGGAGAGCACGAGCAGTACTTCGGG"));
 
 
         IlluminaQualityInterpretationStrategy ill = new IlluminaQualityInterpretationStrategy((byte) 25);
Binary files /tmp/5_yOnfIyun/mitcr-1.0.2/src/test/resources/o_good_flex1.txt.gz and /tmp/kGPchmFFbO/mitcr-1.0.3/src/test/resources/o_good_flex1.txt.gz differ
Binary files /tmp/5_yOnfIyun/mitcr-1.0.2/src/test/resources/o_good_flex2.txt.gz and /tmp/kGPchmFFbO/mitcr-1.0.3/src/test/resources/o_good_flex2.txt.gz differ
Binary files /tmp/5_yOnfIyun/mitcr-1.0.2/src/test/resources/o_good_jprimer1.txt.gz and /tmp/kGPchmFFbO/mitcr-1.0.3/src/test/resources/o_good_jprimer1.txt.gz differ
Binary files /tmp/5_yOnfIyun/mitcr-1.0.2/src/test/resources/o_good_jprimer2.txt.gz and /tmp/kGPchmFFbO/mitcr-1.0.3/src/test/resources/o_good_jprimer2.txt.gz differ