diff -Nru blasr-5.3/cram.mk blasr-5.3+0/cram.mk --- blasr-5.3/cram.mk 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/cram.mk 2016-12-16 01:59:59.000000000 +0000 @@ -1,18 +1,27 @@ FAST_CTESTS := \ +ctest/ecoli.t \ +ctest/fastMaxInterval.t \ +ctest/aggressiveIntervalCut.t \ +ctest/multipart.t \ ctest/affineAlign.t ctest/bamOut.t ctest/ccsH5.t ctest/filtercriteria.t ctest/m0-5.t \ -ctest/aggressiveIntervalCut.t ctest/fofn.t ctest/multipart.t \ +ctest/fofn.t \ ctest/alignScore.t ctest/hitpolicy.t ctest/noSplitSubreads.t \ -ctest/bamIn.t ctest/fastMaxInterval.t ctest/open_fail.t ctest/verbose.t ctest/deterministic.t +ctest/bamIn.t ctest/open_fail.t ctest/verbose.t ctest/deterministic.t MILD_CTESTS := \ - ctest/bug25766.t ctest/holeNumbers.t + ctest/concordant.t ctest/bug25766.t ctest/holeNumbers.t -SLOW_CTESTS := ctest/bug25328.t ctest/useccsallLargeGenome.t +SLOW_CTESTS := ctest/bug25328.t # XXX: following tests sidelined, needs bam input after --sam option removed -# FAST: ctest/ecoli.t -# MILD: ctest/useccsallBestN1.t ctest/concordant.t +# MILD: ctest/useccsallBestN1.t + + +# sidelined because of changes in directories +# +# needed to restore /mnt/data3/vol53/2450530/0014 +# SLOW ctest/useccsallLargeGenome.t #BLASR_PATH=/mnt/secondary/builds/full/3.0.0/prod/current-build_smrtanalysis/private/otherbins/internalall/bin/ #export BLASR_PATH diff -Nru blasr-5.3/ctest/aggressiveIntervalCut.t blasr-5.3+0/ctest/aggressiveIntervalCut.t --- blasr-5.3/ctest/aggressiveIntervalCut.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/aggressiveIntervalCut.t 2016-12-16 01:59:59.000000000 +0000 @@ -3,8 +3,8 @@ Test --aggressiveIntervalCut. $ rm -f $TMP1 - $ BASFILE=/mnt/data3/vol53/2450598/0001/Analysis_Results/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5 - $ REFFA=/mnt/secondary/Smrtpipe/repository/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta + $ BASFILE=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest/data/aggressiveIntervalCut/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5 + $ REFFA=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest/data/references/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta $ $EXEC $BASFILE $REFFA --holeNumbers 1--100 --out $TMP1 --aggressiveIntervalCut [INFO] * [blasr] started. (glob) [INFO] * [blasr] ended. (glob) diff -Nru blasr-5.3/ctest/concordant.t blasr-5.3+0/ctest/concordant.t --- blasr-5.3/ctest/concordant.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/concordant.t 2016-12-16 01:59:59.000000000 +0000 @@ -2,29 +2,13 @@ $ . $TESTDIR/setup.sh Test --concordant - $ rm -rf $OUTDIR/concordant_subset.bam - $ rm -rf $OUTDIR/concordant_subset.sam - $ $EXEC $DATDIR/ecoli_lp.fofn $DATDIR/ecoli_reference.fasta --concordant --refineConcordantAlignments --bam --out $OUTDIR/concordant_subset.bam --nproc 12 --holeNumbers 1--10000 --sa $DATDIR/ecoli_reference.sa + $ rm -rf $OUTDIR/concordant_subset.sam $OUTDIR/tmp1 $OUTDIR/tmp2 + $ $EXEC $DATDIR/ecoli_lp.fofn $DATDIR/ecoli_reference.fasta --concordant --refineConcordantAlignments -m 4 --out $OUTDIR/concordant_subset.m4 --nproc 12 --holeNumbers 1--10000 --sa $DATDIR/ecoli_reference.sa [INFO]* (glob) [INFO]* (glob) - $ $SAMTOOLS view $OUTDIR/concordant_subset.bam > $OUTDIR/concordant_subset.sam - $ sed -n 6,110864p $OUTDIR/concordant_subset.sam > $OUTDIR/tmp1 - $ sort $OUTDIR/tmp1 > $OUTDIR/tmp11 - $ sed -n 6,110864p $STDDIR/$UPDATEDATE/concordant_subset.sam > $OUTDIR/tmp2 - $ sort $OUTDIR/tmp2 > $OUTDIR/tmp22 - $ diff $OUTDIR/tmp11 $OUTDIR/tmp22 - $ rm -rf $OUTDIR/tmp1 $OUTDIR/tmp2 $OUTDIR/tmp11 $OUTDIR/tmp22 -#2014_05_28 --> changelist 135254, use MAX_BAND_SIZE to contrain GuidedAlign -#2014_08_21 --> changelist 138516, added YS, YE, ZM tags. -#2014_08_28 --> changelist 139176, update SAM MD5 -#2014_09_12 --> changelist 140410, changed the default value of '--concordantTemplate' from 'longestsubread' to 'typicalsubread' -#2014_09_17 --> changelist 140573, changed SDPFragment LessThan to make sure blasr compiled with gcc 4.4 and 4.8 can produce identical results. -#2014_10_16 --> changelist 141378, changed the default value of '--concordantTemplate' from 'typicalsubread' to 'mediansubread' -#2015_03_01 --> changelist 146599, reads from the same movie should have unique readGroupId -#2015_03_28 --> changelist 148101, 148080 updated read group id, 148100 updated TLEN -#2015_04_09 --> changelist 148796, updated read group id -#2015_04_25 --> changelist 149721, update CIGAR string, replace M with X=. -#2015_04_25 --> changelist ?, force refine all concordant alignments + $ sort $OUTDIR/concordant_subset.m4 > $OUTDIR/tmp1 +Updated in 2016_10_05 --> changed output format from sam to m4, isolate concordant tests from file format tests + $ diff $OUTDIR/tmp1 $STDDIR/2016_10_05/concordant_subset.m4 Test --concordant FMR1 case (the 'typical subread' is selected as template for concordant mapping) $ FOFN=$DATDIR/FMR1_concordant.fofn @@ -33,3 +17,16 @@ [INFO]* (glob) [INFO]* (glob) $ diff $OUTDIR/FMR1_zmw_37927.m4 $STDDIR/$UPDATEDATE/FMR1_zmw_37927.m4 + +#History +#2014_05_28 --> changelist 135254, use MAX_BAND_SIZE to contrain GuidedAlign +#2014_08_21 --> changelist 138516, added YS, YE, ZM tags. +#2014_08_28 --> changelist 139176, update SAM MD5 +#2014_09_12 --> changelist 140410, changed the default value of '--concordantTemplate' from 'longestsubread' to 'typicalsubread' +#2014_09_17 --> changelist 140573, changed SDPFragment LessThan to make sure blasr compiled with gcc 4.4 and 4.8 can produce identical results. +#2014_10_16 --> changelist 141378, changed the default value of '--concordantTemplate' from 'typicalsubread' to 'mediansubread' +#2015_03_01 --> changelist 146599, reads from the same movie should have unique readGroupId +#2015_03_28 --> changelist 148101, 148080 updated read group id, 148100 updated TLEN +#2015_04_09 --> changelist 148796, updated read group id +#2015_04_25 --> changelist 149721, update CIGAR string, replace M with X=. +#2015_11_09 --> changelist 167117, added -refineConcordantAlignments diff -Nru blasr-5.3/ctest/ecoli.t blasr-5.3+0/ctest/ecoli.t --- blasr-5.3/ctest/ecoli.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/ecoli.t 2016-12-16 01:59:59.000000000 +0000 @@ -13,10 +13,9 @@ [INFO]* (glob) [INFO]* (glob) - $ $SAMTOOLS view $OUTDIR/ecoli_subset.bam > $OUTDIR/ecoli_subset.sam - $ sed -n '5,$ p' $OUTDIR/ecoli_subset.sam | sort | cut -f 1--11 > $TMP1 - $ sed -n '5,$ p' $STDDIR/$UPDATEDATE/ecoli_subset.sam | sort | cut -f 1--11 > $TMP2 - $ diff $TMP1 $TMP2 - $ rm $TMP1 $TMP2 + $ $SAMTOOLS view -h $OUTDIR/ecoli_subset.bam > $OUTDIR/ecoli_subset.sam + $ sed -n '5,$ p' $OUTDIR/ecoli_subset.sam | sort | cut -f 1-11 > $OUTDIR/ecoli_subset_out + $ sed -n '5,$ p' $STDDIR/2016_10_20/ecoli_subset.sam | sort | cut -f 1-11 > $OUTDIR/ecoli_subset_std + $ diff $OUTDIR/ecoli_subset_out $OUTDIR/ecoli_subset_std # 2015_03_08 --> changelist 148101, 148080 updated read group id; 148100 updated TLEN # 2015_04_09 --> changelist 148796, updated read group id diff -Nru blasr-5.3/ctest/fastMaxInterval.t blasr-5.3+0/ctest/fastMaxInterval.t --- blasr-5.3/ctest/fastMaxInterval.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/fastMaxInterval.t 2016-12-16 01:59:59.000000000 +0000 @@ -3,8 +3,8 @@ Test --fastMaxInterval. $ rm -f $TMP1 - $ BASFILE=/mnt/data3/vol53/2450598/0001/Analysis_Results/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5 - $ REFFA=/mnt/secondary/Smrtpipe/repository/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta + $ BASFILE=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest/data/aggressiveIntervalCut/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5 + $ REFFA=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest/data/references/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta $ $EXEC $BASFILE $REFFA --holeNumbers 1--100 --out $TMP1 --fastMaxInterval [INFO] * [blasr] started. (glob) [INFO] * [blasr] ended. (glob) diff -Nru blasr-5.3/ctest/multipart.t blasr-5.3+0/ctest/multipart.t --- blasr-5.3/ctest/multipart.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/multipart.t 2016-12-16 01:59:59.000000000 +0000 @@ -4,8 +4,8 @@ Test input.fofn containing a new bas.h5 file. Note that the new bas.h5 file does not contain any /PulseData, instead contains /MultiPart/Parts. $ rm -f $TMP1 - $ BASFILE=/mnt/data3/vol53/2450598/0001/Analysis_Results/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5 - $ REFFA=/mnt/secondary/Smrtpipe/repository/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta + $ BASFILE=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest/data/aggressiveIntervalCut/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5 + $ REFFA=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest/data/references/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta $ $EXEC $BASFILE $REFFA --holeNumbers 1--100 --out $TMP1 [INFO] * [blasr] started. (glob) [INFO] * [blasr] ended. (glob) diff -Nru blasr-5.3/ctest/noSplitSubreads.t blasr-5.3+0/ctest/noSplitSubreads.t --- blasr-5.3/ctest/noSplitSubreads.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/noSplitSubreads.t 2016-12-16 01:59:59.000000000 +0000 @@ -16,3 +16,37 @@ [INFO]* (glob) $ sort $OUTDIR/lambda_bax_noSplitSubreads_tmp_subset.m4 > $OUTDIR/lambda_bax_noSplitSubreads_subset.m4 $ diff $OUTDIR/lambda_bax_noSplitSubreads_subset.m4 $STDDIR/lambda_bax_noSplitSubreads_subset.m4 + +# Test key command of unrolled resequencing, check bam header and alignments in output + $ outbam=$OUTDIR/unrolled-4mer.bam + $ outsam=$OUTDIR/unrolled-4mer.sam + $ query=$DATDIR/unrolled/m54006_151021_185942.subreadset.xml + $ ref=$DATDIR/unrolled/All4mer_V2_11_V2_13_V2_15_V2_44_circular_72x_l50256.fasta + $ stdsam=$STDDIR/unrolled-4mer.sam + $ rm -rf $outbam $outsam + $ $EXEC $query $ref --out $outbam --noSplitSubreads --fastMaxInterval --bam + [INFO]* (glob) + [INFO]* (glob) + $ $SAMTOOLS view -h $outbam -o $outsam + $ grep -v '^@PG' $outsam > $TMP1 && grep -v '^@PG' $stdsam > $TMP2 && diff $TMP1 $TMP2 + $ grep '@RG' $outsam + @RG\tID:e6043908* (glob) + $ grep 'RG:Z:e6043908' $outsam |wc -l + 4 + + + $ query=$DATDIR/unrolled/m54006_151021_185942.subreads.bam + $ outbam=$OUTDIR/unrolled-4mer-bam-in.bam + $ outsam=$OUTDIR/unrolled-4mer-bam-in.sam + $ rm -rf $outbam $outsam + $ $EXEC $query $ref --out $outbam --noSplitSubreads --fastMaxInterval --bam + [INFO]* (glob) + [INFO]* (glob) + $ $SAMTOOLS view -h $outbam -o $outsam + $ grep -v '^@PG' $outsam > $TMP1 && grep -v '^@PG' $stdsam > $TMP2 && diff $TMP1 $TMP2 + $ grep '@RG' $outsam + @RG\tID:e6043908* (glob) + $ grep 'RG:Z:e6043908' $outsam |wc -l + 4 + + diff -Nru blasr-5.3/ctest/useccsallBestN1.t blasr-5.3+0/ctest/useccsallBestN1.t --- blasr-5.3/ctest/useccsallBestN1.t 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/ctest/useccsallBestN1.t 2016-12-16 01:59:59.000000000 +0000 @@ -5,7 +5,7 @@ $ $EXEC $DATDIR/ccstest.fofn $DATDIR/ccstest_ref.fasta --bestn 1 --useccsall --bam --out $OUTDIR/useccsall.bam --holeNumbers 76772 [INFO]* (glob) [INFO]* (glob) - $ $SAMTOOLS view $OUTDIR/useccsall.bam > $OUTDIR/useccsall.sam + $ $SAMTOOLS view -h $OUTDIR/useccsall.bam > $OUTDIR/useccsall.sam $ sed -n '9,$ p' $OUTDIR/useccsall.sam |cut -f 1-4 > $TMP1 $ sed -n '9,$ p' $STDDIR/$UPDATEDATE/useccsall.sam | cut -f 1-4 > $TMP2 $ diff $TMP1 $TMP2 diff -Nru blasr-5.3/debian/changelog blasr-5.3+0/debian/changelog --- blasr-5.3/debian/changelog 2016-11-29 17:33:15.000000000 +0000 +++ blasr-5.3+0/debian/changelog 2016-12-24 01:51:41.000000000 +0000 @@ -1,8 +1,17 @@ -blasr (5.3-1build1) zesty; urgency=medium +blasr (5.3+0-1) unstable; urgency=medium - * Rebuild against new hdf5 + * Imported Upstream version 5.3+0 (corresponds to smrtanalysis-4.0.0 tag) + * Refresh patches - -- Iain Lane Tue, 29 Nov 2016 17:33:15 +0000 + -- Afif Elghraoui Fri, 23 Dec 2016 17:50:11 -0800 + +blasr (5.3-2) unstable; urgency=medium + + * Use pbseqlib metapackage rather than depending on individual libraries + * Build with pbbam (Closes: #848751, #848541) + * Build bax2bam and bam2bax + + -- Afif Elghraoui Tue, 20 Dec 2016 02:02:51 -0800 blasr (5.3-1) unstable; urgency=medium diff -Nru blasr-5.3/debian/control blasr-5.3+0/debian/control --- blasr-5.3/debian/control 2016-10-24 00:40:38.000000000 +0000 +++ blasr-5.3+0/debian/control 2016-12-20 10:01:23.000000000 +0000 @@ -6,11 +6,12 @@ Build-Depends: debhelper (>= 9), python, + cmake, + libboost-dev, libhdf5-dev, zlib1g-dev, - libblasr-dev, - libpbdata-dev, - libpbihdf-dev, + libpbseq-dev (>= 0~20160912), + libpbbam-dev, Standards-Version: 3.9.8 Homepage: https://github.com/PacificBiosciences/blasr Vcs-Git: https://anonscm.debian.org/git/debian-med/blasr.git @@ -21,9 +22,8 @@ Depends: ${shlibs:Depends}, ${misc:Depends}, - libblasr, - libpbdata, - libpbihdf, + libpbseq (>= 0~20160912), + libpbbam, Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. diff -Nru blasr-5.3/debian/install blasr-5.3+0/debian/install --- blasr-5.3/debian/install 2015-07-27 08:11:25.000000000 +0000 +++ blasr-5.3+0/debian/install 2016-12-20 10:01:22.000000000 +0000 @@ -7,3 +7,5 @@ utils/toAfg usr/bin utils/sawriter usr/bin utils/sdpMatcher usr/bin +utils/bax2bam/bin/* usr/bin +utils/bam2bax/bin/* usr/bin diff -Nru blasr-5.3/debian/patches/cmake-utils.patch blasr-5.3+0/debian/patches/cmake-utils.patch --- blasr-5.3/debian/patches/cmake-utils.patch 1970-01-01 00:00:00.000000000 +0000 +++ blasr-5.3+0/debian/patches/cmake-utils.patch 2016-12-24 00:56:59.000000000 +0000 @@ -0,0 +1,25 @@ +Description: Fix passage of boost header paths to cmake +Author: Afif Elghraoui +Forwarded: no +--- blasr.orig/utils/bax2bam/makefile ++++ blasr/utils/bax2bam/makefile +@@ -10,7 +10,7 @@ + all: ${CURDIR}/src/* ${CURDIR}/tests/src/* + @mkdir -p ${CURDIR}/build && \ + cd ${CURDIR}/build && \ +- cmake -DBOOST_ROOT=${BOOST_ROOT} \ ++ cmake -DBoost_INCLUDE_DIRS=${BOOST_INC} \ + -DPacBioBAM_INCLUDE_DIRS=${PBBAM_INC} \ + -DHTSLIB_INCLUDE_DIRS=${HTSLIB_INC} \ + -DPacBioBAM_LIBRARIES=${PBBAM_LIB}/libpbbam${SH_LIB_EXT} \ +--- blasr.orig/utils/bam2bax/makefile ++++ blasr/utils/bam2bax/makefile +@@ -10,7 +10,7 @@ + all: ${CURDIR}/src/*.cpp ${CURDIR}/src/*.h ${CURDIR}/tests/src/*.cpp ${CURDIR}/tests/src/*.h + @mkdir -p ${CURDIR}/build && \ + cd ${CURDIR}/build && \ +- cmake -DBOOST_ROOT=${BOOST_ROOT} \ ++ cmake -DBoost_INCLUDE_DIRS=${BOOST_INC} \ + -DPacBioBAM_INCLUDE_DIRS=${PBBAM_INC} \ + -DHTSLIB_INCLUDE_DIRS=${HTSLIB_INC} \ + -DPacBioBAM_LIBRARIES=${PBBAM_LIB}/libpbbam${SH_LIB_EXT} \ diff -Nru blasr-5.3/debian/patches/disable-gtest.patch blasr-5.3+0/debian/patches/disable-gtest.patch --- blasr-5.3/debian/patches/disable-gtest.patch 1970-01-01 00:00:00.000000000 +0000 +++ blasr-5.3+0/debian/patches/disable-gtest.patch 2016-12-20 10:01:22.000000000 +0000 @@ -0,0 +1,28 @@ +Description: temporarily disable gtests for bax2bam and bam2bax + We should make use of the packaged gtest; without additional effort, + the build system doesn't find it. +Author: Afif Elghraoui +Forwarded: not-needed +Last-Update: 2016-12-20 +--- blasr.orig/utils/bam2bax/CMakeLists.txt ++++ blasr/utils/bam2bax/CMakeLists.txt +@@ -14,7 +14,7 @@ + ) + + # build-time options +-option(Bam2Bax_build_tests "Build Bam2Bax's unit tests." ON) ++option(Bam2Bax_build_tests "Build Bam2Bax's unit tests." OFF) + + # main project paths + set(Bam2Bax_RootDir ${Bam2Bax_SOURCE_DIR}) +--- blasr.orig/utils/bax2bam/CMakeLists.txt ++++ blasr/utils/bax2bam/CMakeLists.txt +@@ -14,7 +14,7 @@ + ) + + # build-time options +-option(Bax2BAM_build_tests "Build Bax2BAM's unit tests." ON) ++option(Bax2BAM_build_tests "Build Bax2BAM's unit tests." OFF) + + # main project paths + set(Bax2Bam_RootDir ${Bax2Bam_SOURCE_DIR}) diff -Nru blasr-5.3/debian/patches/series blasr-5.3+0/debian/patches/series --- blasr-5.3/debian/patches/series 2015-12-21 21:59:00.000000000 +0000 +++ blasr-5.3+0/debian/patches/series 2016-12-20 10:01:22.000000000 +0000 @@ -0,0 +1,2 @@ +disable-gtest.patch +cmake-utils.patch diff -Nru blasr-5.3/debian/rules blasr-5.3+0/debian/rules --- blasr-5.3/debian/rules 2016-10-24 02:19:28.000000000 +0000 +++ blasr-5.3+0/debian/rules 2016-12-20 10:01:23.000000000 +0000 @@ -2,25 +2,55 @@ include /usr/share/dpkg/default.mk +export VERBOSE=1 # for cmake +export SH_LIB_EXT=.so + export HDF5_INC=/usr/include/hdf5/serial export HDF5_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial +export BOOST_INC=/usr/include/boost +export HTSLIB_INC=/usr/include/htslib +export HTSLIB_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export PBBAM_INC=/usr/include +export PBBAM_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export PBDATA_ROOT_DIR=/usr/include/pbseq +export LIBBLASR_INC=$(PBDATA_ROOT_DIR)/alignment +export LIBBLASR_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export LIBPBDATA_INC=$(PBDATA_ROOT_DIR)/pbdata +export LIBPBDATA_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export LIBPBIHDF_INC=$(PBDATA_ROOT_DIR)/hdf +export LIBPBIHDF_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) -PBSEQ_BASE=/usr/include/pbseq -export LIBBLASR_INC=$(PBSEQ_BASE)/alignment -export LIBPBDATA_INC=$(PBSEQ_BASE)/pbdata -export LIBPBIHDF_INC=$(PBSEQ_BASE)/hdf - +# CPPFLAGS apparently aren't exported for bam2bax/bax2bam +export DEB_CXXFLAGS_MAINT_PREPEND = $(CPPFLAGS) -I$(PBDATA_ROOT_DIR) %: dh $@ --parallel override_dh_auto_configure: - ./configure.py --no-pbbam --shared + ./configure.py --shared + +override_dh_auto_build: main bax2bam bam2bax; + +.PHONY: main +main: + dh_auto_build + +.PHONY: bax2bam +bax2bam: utils/bax2bax/bin/bax2bam +utils/bax2bax/bin/bax2bam: + $(MAKE) -C utils/bax2bam + +.PHONY: bam2bax +bam2bax: utils/bam2bax/bin/bam2bax +utils/bam2bax/bin/bam2bax: + $(MAKE) -C utils/bam2bax # Tests require data not available in the source distribution override_dh_auto_test: ; override_dh_auto_clean: override_dh_auto_configure $(MAKE) clean + $(MAKE) -C utils/bam2bax clean + $(MAKE) -C utils/bax2bam clean # This is created by configure.py $(RM) defines.mk diff -Nru blasr-5.3/debian/TODO blasr-5.3+0/debian/TODO --- blasr-5.3/debian/TODO 2016-10-24 00:40:13.000000000 +0000 +++ blasr-5.3+0/debian/TODO 2016-12-20 10:01:23.000000000 +0000 @@ -2,6 +2,4 @@ * Update manpages -* build bax2bam and bam2bax - -* Look into building with pbbam +* run test suite for bax2bam and bam2bax diff -Nru blasr-5.3/iblasr/MappingParameters.h blasr-5.3+0/iblasr/MappingParameters.h --- blasr-5.3/iblasr/MappingParameters.h 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/iblasr/MappingParameters.h 2016-12-16 01:59:59.000000000 +0000 @@ -142,7 +142,9 @@ bool refineConcordantAlignments; int flankSize; bool useRegionTable; + bool setIgnoreRegions; bool useHQRegionTable; + bool setIgnoreHQRegions; bool printUnaligned; bool noPrintUnalignedSeqs; // print unaligned reads names only. string unalignedFileName; @@ -311,7 +313,9 @@ refineConcordantAlignments=false; flankSize=40; useRegionTable = true; + setIgnoreRegions = false; useHQRegionTable=true; + setIgnoreHQRegions = false; printUnaligned = false; unalignedFileName = ""; noPrintUnalignedSeqs = false; @@ -454,6 +458,9 @@ // // Fix all logical incompatibilities with parameters. // + if (setIgnoreRegions) { useRegionTable = false; } + if (setIgnoreHQRegions) { useHQRegionTable = false; } + if (nowarp) { warp = false; } @@ -534,6 +541,14 @@ useRegionTable = true; readSeparateRegionTable = true; } + + bool isHDFFile = (queryFileType == FileType::HDFPulse or + queryFileType == FileType::HDFBase or + queryFileType == FileType::HDFCCSONLY); + if ((setIgnoreRegions or setIgnoreHQRegions) and not isHDFFile) { + cout << "ERROR: query must be HDF files in order to set ignoreRegions or ignoreHQRegions." << std::endl; + exit(1); + } if (ccsFofnFileName != "") { readSeparateCcsFofn = true; } @@ -699,6 +714,11 @@ return ReadType::CCS; } if (queryFileType == FileType::PBBAM) { + if (not mapSubreadsSeparately) { + // specifal case: blasr subread.bam ref.fa --noSplitSubreads + // input type seems like subread while infact is polymerase + return ReadType::POLYMERASE; + } // Read type in BAM may be CCS, SUBREAD, HQREGION or POLYMERASE. // Determine it later. return ReadType::UNKNOWN; @@ -706,7 +726,11 @@ if (mapSubreadsSeparately) { return ReadType::SUBREAD; } else { - if (useHQRegionTable) { + if (useHQRegionTable and + (queryFileType == FileType::HDFCCSONLY or + queryFileType == FileType::HDFBase or + queryFileType == FileType::HDFPulse)) { + // Only HDF files can contain region table. return ReadType::HQREGION; } else { return ReadType::POLYMERASE; diff -Nru blasr-5.3/iblasr/RegisterBlasrOptions.h blasr-5.3+0/iblasr/RegisterBlasrOptions.h --- blasr-5.3/iblasr/RegisterBlasrOptions.h 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/iblasr/RegisterBlasrOptions.h 2016-12-16 01:59:59.000000000 +0000 @@ -83,8 +83,8 @@ clp.RegisterIntOption("-maxScore", ¶ms.maxScore, "", CommandLineParser::Integer); clp.RegisterStringOption("-bwt", ¶ms.bwtFileName, ""); clp.RegisterIntOption("m", ¶ms.printFormat, "", CommandLineParser::NonNegativeInteger); - clp.RegisterFlagOption("-sam", ¶ms.printSAM, ""); #ifdef USE_PBBAM + clp.RegisterFlagOption("-sam", ¶ms.printSAM, ""); clp.RegisterFlagOption("-bam", ¶ms.printBAM, ""); #endif clp.RegisterStringOption("-clipping", ¶ms.clippingString, ""); @@ -135,8 +135,9 @@ clp.RegisterIntOption("-flankSize", ¶ms.flankSize, "", CommandLineParser::NonNegativeInteger); clp.RegisterStringOption("-titleTable", ¶ms.titleTableName, ""); clp.RegisterFlagOption("-useSensitiveSearch", ¶ms.doSensitiveSearch, ""); - clp.RegisterFlagOption("-ignoreRegions", ¶ms.useRegionTable, ""); - clp.RegisterFlagOption("-ignoreHQRegions", ¶ms.useHQRegionTable, ""); + // ignoreRegions or ignoreHQRegions implies region table must exist (i.e., query is HDF). + clp.RegisterFlagOption("-ignoreRegions", ¶ms.setIgnoreRegions, ""); + clp.RegisterFlagOption("-ignoreHQRegions", ¶ms.setIgnoreHQRegions, ""); clp.RegisterFlagOption("-computeAlignProbability", ¶ms.computeAlignProbability, ""); clp.RegisterStringOption("-unaligned", ¶ms.unalignedFileName, ""); // Print unaligned reads names only @@ -289,8 +290,8 @@ << " Use no/hard/subread/soft clipping, ONLY for SAM/BAM output."<< endl << " --printSAMQV (false)" << endl << " Print quality values to SAM output." << endl - << " --cigarUseSeqMatch (false)" << endl - << " CIGAR strings in SAM/BAM output use '=' and 'X' to represent sequence match and mismatch instead of 'M'." << endl << endl +// << " --cigarUseSeqMatch (false)" << endl +// << " CIGAR strings in SAM/BAM output use '=' and 'X' to represent sequence match and mismatch instead of 'M'." << endl << endl << " Options for anchoring alignment regions. This will have the greatest effect on speed and sensitivity." << endl << " --minMatch m (12) " << endl << " Minimum seed length. Higher minMatch will speed up alignment, " << endl diff -Nru blasr-5.3/makefile blasr-5.3+0/makefile --- blasr-5.3/makefile 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/makefile 2016-12-16 01:59:59.000000000 +0000 @@ -76,6 +76,10 @@ ${MAKE} -f cram.mk cramfast ${MAKE} -C utils cramfast +crammild: blasr utils + ${MAKE} -f cram.mk crammild + ${MAKE} -C utils crammild + gtest: blasr # This requires the submodule to be configured with gtest. ${MAKE} -C libcpp gtest diff -Nru blasr-5.3/utils/bam2bax/BUILD.txt blasr-5.3+0/utils/bam2bax/BUILD.txt --- blasr-5.3/utils/bam2bax/BUILD.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bam2bax/BUILD.txt 2016-12-16 01:59:59.000000000 +0000 @@ -9,6 +9,11 @@ Build instructions for users: + + If pbbam and htslib are prebuilt and included in blasr/defines.mk, + set PacBioBAM_INCLUDE_DIRS, HTSLIB_INCLUDE_DIRS, PacBioBAM_LIBRARIES + and HTSLIB_LIBRARIES as below. Otherwise, set PacBioBAM_RootDir instead. + $ cd $ mkdir build; cd build; $ cmake -DPacBioBAM_INCLUDE_DIRS= \ @@ -26,23 +31,38 @@ -DHDF5_LIBRARIES= \ -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \ ../ - $ make $ ../tests/bin/test_bam2bax # to test bam2bax exe -# e.g., -#cmake -DPacBioBAM_INCLUDE_DIRS=$smrtanalysis/bioinformatics/lib/cpp/pbbam/include \ -# -DHTSLIB_INCLUDE_DIRS=$smrtanalysis/bioinformatics/lib/cpp/htslib \ -# -DPacBioBAM_LIBRARIES=$smrtanalysis/bioinformatics/lib/cpp/pbbam/lib/libpbbam.a \ -# -DHTSLIB_LIBRARIES=$smrtanalysis/bioinformatics/lib/cpp/htslib/libhts.a \ -# -DPBDATA_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata \ -# -DPBDATA_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata/libpbdata.a \ -# -DPBIHDF_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf \ -# -DPBIHDF_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf/libpbihdf.a \ -# -DBLASR_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/ \ -# -DBLASR_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/libblasr.a \ -# -DHDF5_INCLUDE_DIRS=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/include \ -# -DHDF5_CPP_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5_cpp.a \ -# -DHDF5_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5.a \ -# -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \ -# ../ + + An example: + $ cmake -DPacBioBAM_INCLUDE_DIRS=$smrtanalysis/bioinformatics/lib/cpp/pbbam/include \ + -DHTSLIB_INCLUDE_DIRS=$smrtanalysis/bioinformatics/lib/cpp/htslib \ + -DPacBioBAM_LIBRARIES=$smrtanalysis/bioinformatics/lib/cpp/pbbam/lib/libpbbam.a \ + -DHTSLIB_LIBRARIES=$smrtanalysis/bioinformatics/lib/cpp/htslib/libhts.a \ + -DPBDATA_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata \ + -DPBDATA_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata/libpbdata.a \ + -DPBIHDF_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf \ + -DPBIHDF_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf/libpbihdf.a \ + -DBLASR_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/ \ + -DBLASR_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/libblasr.a \ + -DHDF5_INCLUDE_DIRS=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/include \ + -DHDF5_CPP_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5_cpp.a \ + -DHDF5_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5.a \ + -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \ + ../ + + Alternatively: + $ cmake \ + -DPacBioBAM_RootDir=$smrtanalsis/bioinformatics/lib/cpp/pbbam \ + -DPBDATA_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata \ + -DPBDATA_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata/libpbdata.a \ + -DPBIHDF_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf \ + -DPBIHDF_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf/libpbihdf.a \ + -DBLASR_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/ \ + -DBLASR_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/libblasr.a \ + -DHDF5_INCLUDE_DIRS=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/include \ + -DHDF5_CPP_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5_cpp.a \ + -DHDF5_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5.a \ + -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \ + ../ diff -Nru blasr-5.3/utils/bam2bax/CMakeLists.txt blasr-5.3+0/utils/bam2bax/CMakeLists.txt --- blasr-5.3/utils/bam2bax/CMakeLists.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bam2bax/CMakeLists.txt 2016-12-16 01:59:59.000000000 +0000 @@ -66,8 +66,15 @@ if (NOT PacBioBAM_INCLUDE_DIRS OR NOT PacBioBAM_LIBRARIES OR NOT HTSLIB_INCLUDE_DIRS OR NOT HTSLIB_LIBRARIES) - set(PacBioBAM_RootDir ${Bam2Bax_RootDir}/../../../../../lib/cpp/pbbam) + set(PacBioBAM_LIBRARIES ) + set(PacBioBAM_INCLUDE_DIRS ) + set(HTSLIB_INCLUDE_DIRS ) + set(HTSLIB_LIBRARIES ) + if (NOT PacBioBAM_RootDir) + message ("Must either set (PacBioBAM_INCLUDE_DIRS, PacBioBAM_LIBRARIES, HTSLIB_INCLUDE_DIRS, and HTSLIB_LIBRARIES) or PacBioBAM_RootDir!") + endif() add_subdirectory(${PacBioBAM_RootDir} external/build/pbbam) + set(PBBAM_LINK_FLAG pbbam) endif() if (NOT Boost_INCLUDE_DIRS) @@ -130,4 +137,3 @@ add_subdirectory(${GTEST_SRC_DIR} external/gtest/build) add_subdirectory(tests) endif() - diff -Nru blasr-5.3/utils/bam2bax/makefile blasr-5.3+0/utils/bam2bax/makefile --- blasr-5.3/utils/bam2bax/makefile 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bam2bax/makefile 2016-12-16 01:59:59.000000000 +0000 @@ -4,6 +4,9 @@ -include ${CURDIR}/../../defines.mk include ${SRCDIR}/../../rules.mk +# If pbbam and htslib are prebuilt and included in defines.mk, +# set PacBioBAM_INCLUDE_DIRS, HTSLIB_INCLUDE_DIRS, PacBioBAM_LIBRARIES +# and HTSLIB_LIBRARIES as below. Otherwise, set PacBioBAM_RootDir instead. all: ${CURDIR}/src/*.cpp ${CURDIR}/src/*.h ${CURDIR}/tests/src/*.cpp ${CURDIR}/tests/src/*.h @mkdir -p ${CURDIR}/build && \ cd ${CURDIR}/build && \ @@ -25,6 +28,25 @@ ../ && \ make +# If pbbam is not prebuilt, just set PacBioBAM_RootDir +#all: ${CURDIR}/src/*.cpp ${CURDIR}/src/*.h ${CURDIR}/tests/src/*.cpp ${CURDIR}/tests/src/*.h +# @mkdir -p ${CURDIR}/build && \ +# cd ${CURDIR}/build && \ +# cmake -DBOOST_ROOT=${BOOST_ROOT} \ +# -DPacBioBAM_RootDir=/home/UNIXHOME/yli/git/depot/software/smrtanalysis/bioinformatics/lib/cpp/pbbam \ +# -DPBDATA_INCLUDE_DIRS=${LIBPBDATA_INC} \ +# -DPBDATA_LIBRARIES=${LIBPBDATA_LIB}/libpbdata${SH_LIB_EXT} \ +# -DPBIHDF_INCLUDE_DIRS=${LIBPBIHDF_INC} \ +# -DPBIHDF_LIBRARIES=${LIBPBIHDF_LIB}/libpbihdf${SH_LIB_EXT} \ +# -DBLASR_INCLUDE_DIRS=${LIBBLASR_INC}/ \ +# -DBLASR_LIBRARIES=${LIBBLASR_LIB}/libblasr${SH_LIB_EXT} \ +# -DHDF5_INCLUDE_DIRS=${HDF5_INC} \ +# -DHDF5_CPP_LIBRARIES=${HDF5_LIB}/libhdf5_cpp${SH_LIB_EXT} \ +# -DHDF5_LIBRARIES=${HDF5_LIB}/libhdf5${SH_LIB_EXT} \ +# -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \ +# ../ && \ +# make + clean: @rm -rf ${CURDIR}/bin/ @rm -rf ${CURDIR}/build diff -Nru blasr-5.3/utils/bam2bax/src/CMakeLists.txt blasr-5.3+0/utils/bam2bax/src/CMakeLists.txt --- blasr-5.3/utils/bam2bax/src/CMakeLists.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bam2bax/src/CMakeLists.txt 2016-12-16 01:59:59.000000000 +0000 @@ -51,6 +51,7 @@ else() endif() target_link_libraries(bam2bax + ${PBBAM_LINK_FLAG} ${BLASR_LIBRARIES} ${PBIHDF_LIBRARIES} ${PBDATA_LIBRARIES} @@ -67,6 +68,7 @@ RUNTIME_OUTPUT_DIRECTORY ${Bam2Bax_BinDir} ) target_link_libraries(bam2plx + ${PBBAM_LINK_FLAG} ${BLASR_LIBRARIES} ${PBIHDF_LIBRARIES} ${PBDATA_LIBRARIES} diff -Nru blasr-5.3/utils/bam2bax/tests/CMakeLists.txt blasr-5.3+0/utils/bam2bax/tests/CMakeLists.txt --- blasr-5.3/utils/bam2bax/tests/CMakeLists.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bam2bax/tests/CMakeLists.txt 2016-12-16 01:59:59.000000000 +0000 @@ -74,6 +74,7 @@ target_link_libraries(test_bam2bax gtest gtest_main + ${PBBAM_LINK_FLAG} ${BLASR_LIBRARIES} ${PBIHDF_LIBRARIES} ${PBDATA_LIBRARIES} diff -Nru blasr-5.3/utils/bax2bam/CMakeLists.txt blasr-5.3+0/utils/bax2bam/CMakeLists.txt --- blasr-5.3/utils/bax2bam/CMakeLists.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/CMakeLists.txt 2016-12-16 01:59:59.000000000 +0000 @@ -65,8 +65,15 @@ if (NOT PacBioBAM_INCLUDE_DIRS OR NOT PacBioBAM_LIBRARIES OR NOT HTSLIB_INCLUDE_DIRS OR NOT HTSLIB_LIBRARIES) - set(PacBioBAM_RootDir ${Bax2Bam_RootDir}/../../../../../lib/cpp/pbbam) + set(PacBioBAM_INCLUDE_DIRS ) + set(PacBioBAM_LIBRARIES ) + set(HTSLIB_INCLUDE_DIRS ) + set(HTSLIB_LIBRARIES ) + if (NOT PacBioBAM_RootDir) + message ("Must either set (PacBioBAM_INCLUDE_DIRS, PacBioBAM_LIBRARIES, HTSLIB_INCLUDE_DIRS, and HTSLIB_LIBRARIES) or PacBioBAM_RootDir!") + endif() add_subdirectory(${PacBioBAM_RootDir} external/build/pbbam) + set(PBBAM_LINK_FLAG pbbam) endif() if (NOT Boost_INCLUDE_DIRS) diff -Nru blasr-5.3/utils/bax2bam/makefile blasr-5.3+0/utils/bax2bam/makefile --- blasr-5.3/utils/bax2bam/makefile 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/makefile 2016-12-16 01:59:59.000000000 +0000 @@ -4,6 +4,9 @@ include ${CURDIR}/../../defines.mk include ${SRCDIR}/../../rules.mk +# If pbbam and htslib are prebuilt and included in blasr/defines.mk, +# set PacBioBAM_INCLUDE_DIRS, HTSLIB_INCLUDE_DIRS, PacBioBAM_LIBRARIES +# and HTSLIB_LIBRARIES as below. Otherwise, just set PacBioBAM_RootDir instead. all: ${CURDIR}/src/* ${CURDIR}/tests/src/* @mkdir -p ${CURDIR}/build && \ cd ${CURDIR}/build && \ @@ -25,6 +28,7 @@ ../ && \ make + clean: @rm -rf ${CURDIR}/bin/ @rm -rf ${CURDIR}/build diff -Nru blasr-5.3/utils/bax2bam/src/CMakeLists.txt blasr-5.3+0/utils/bax2bam/src/CMakeLists.txt --- blasr-5.3/utils/bax2bam/src/CMakeLists.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/src/CMakeLists.txt 2016-12-16 01:59:59.000000000 +0000 @@ -45,6 +45,7 @@ else() endif() target_link_libraries(bax2bam + ${PBBAM_LINK_FLAG} ${BLASR_LIBRARIES} ${PBIHDF_LIBRARIES} ${PBDATA_LIBRARIES} diff -Nru blasr-5.3/utils/bax2bam/src/IConverter.cpp blasr-5.3+0/utils/bax2bam/src/IConverter.cpp --- blasr-5.3/utils/bax2bam/src/IConverter.cpp 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/src/IConverter.cpp 2016-12-16 01:59:59.000000000 +0000 @@ -24,13 +24,6 @@ { BamHeader header; - // @HD VN: - // SO:unsorted - // pb: - header.Version("1.5") - .SortOrder("unknown") - .PacBioBamVersion("3.0.2"); - // @RG ID: // DS: READTYPE=[;;BINDINGKIT=;SEQUENCINGKIT=;BASECALLERVERSION=<42>] // PL: PACBIO diff -Nru blasr-5.3/utils/bax2bam/src/main.cpp blasr-5.3+0/utils/bax2bam/src/main.cpp --- blasr-5.3/utils/bax2bam/src/main.cpp 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/src/main.cpp 2016-12-16 01:59:59.000000000 +0000 @@ -65,7 +65,7 @@ readModeGroup.add_option("--ccs") .dest(Settings::Option::ccsMode_) .action("store_true") - .help("Output CCS sequences"); + .help("Output CCS sequences (requires ccs.h5 input)"); parser.add_option_group(readModeGroup); auto featureGroup = optparse::OptionGroup(parser, "Pulse feature options"); diff -Nru blasr-5.3/utils/bax2bam/tests/CMakeLists.txt blasr-5.3+0/utils/bax2bam/tests/CMakeLists.txt --- blasr-5.3/utils/bax2bam/tests/CMakeLists.txt 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/tests/CMakeLists.txt 2016-12-16 01:59:59.000000000 +0000 @@ -69,6 +69,7 @@ target_link_libraries(test_bax2bam gtest gtest_main + ${PBBAM_LINK_FLAG} ${BLASR_LIBRARIES} ${PBIHDF_LIBRARIES} ${PBDATA_LIBRARIES} diff -Nru blasr-5.3/utils/bax2bam/tests/src/test_ccs.cpp blasr-5.3+0/utils/bax2bam/tests/src/test_ccs.cpp --- blasr-5.3/utils/bax2bam/tests/src/test_ccs.cpp 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/tests/src/test_ccs.cpp 2016-12-16 01:59:59.000000000 +0000 @@ -101,9 +101,9 @@ // check BAM header information const BamHeader& header = bamFile.Header(); - EXPECT_EQ(string("1.5"), header.Version()); + EXPECT_EQ(tests::Header_Version, header.Version()); EXPECT_EQ(string("unknown"), header.SortOrder()); - EXPECT_EQ(string("3.0.2"), header.PacBioBamVersion()); + EXPECT_EQ(tests::PacBioBam_Version, header.PacBioBamVersion()); EXPECT_TRUE(header.Sequences().empty()); EXPECT_TRUE(header.Comments().empty()); ASSERT_FALSE(header.Programs().empty()); diff -Nru blasr-5.3/utils/bax2bam/tests/src/TestData.h.in blasr-5.3+0/utils/bax2bam/tests/src/TestData.h.in --- blasr-5.3/utils/bax2bam/tests/src/TestData.h.in 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/tests/src/TestData.h.in 2016-12-16 01:59:59.000000000 +0000 @@ -11,6 +11,8 @@ const std::string Source_Dir = std::string("@Bax2Bam_TestsDir@"); const std::string Bin_Dir = std::string("@CMAKE_CURRENT_BINARY_DIR@"); const std::string Data_Dir = std::string("/pbi/dept/secondary/siv/testdata/bax2bam"); +const std::string Header_Version = std::string("1.1"); +const std::string PacBioBam_Version = std::string("3.0.3"); } // namespace tests diff -Nru blasr-5.3/utils/bax2bam/tests/src/test_hqregions.cpp blasr-5.3+0/utils/bax2bam/tests/src/test_hqregions.cpp --- blasr-5.3/utils/bax2bam/tests/src/test_hqregions.cpp 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/tests/src/test_hqregions.cpp 2016-12-16 01:59:59.000000000 +0000 @@ -104,9 +104,9 @@ // check BAM header information const BamHeader& header = bamFile.Header(); - EXPECT_EQ(string("1.5"), header.Version()); + EXPECT_EQ(string(tests::Header_Version), header.Version()); EXPECT_EQ(string("unknown"), header.SortOrder()); - EXPECT_EQ(string("3.0.2"), header.PacBioBamVersion()); + EXPECT_EQ(string(tests::PacBioBam_Version), header.PacBioBamVersion()); EXPECT_TRUE(header.Sequences().empty()); EXPECT_TRUE(header.Comments().empty()); ASSERT_FALSE(header.Programs().empty()); @@ -261,9 +261,9 @@ // check BAM header information const BamHeader& header = bamFile.Header(); - EXPECT_EQ(string("1.5"), header.Version()); + EXPECT_EQ(tests::Header_Version, header.Version()); EXPECT_EQ(string("unknown"), header.SortOrder()); - EXPECT_EQ(string("3.0.2"), header.PacBioBamVersion()); + EXPECT_EQ(tests::PacBioBam_Version, header.PacBioBamVersion()); EXPECT_TRUE(header.Sequences().empty()); EXPECT_TRUE(header.Comments().empty()); ASSERT_FALSE(header.Programs().empty()); diff -Nru blasr-5.3/utils/bax2bam/tests/src/test_polymerase.cpp blasr-5.3+0/utils/bax2bam/tests/src/test_polymerase.cpp --- blasr-5.3/utils/bax2bam/tests/src/test_polymerase.cpp 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/tests/src/test_polymerase.cpp 2016-12-16 01:59:59.000000000 +0000 @@ -87,9 +87,9 @@ // check BAM header information const BamHeader& header = bamFile.Header(); - EXPECT_EQ(string("1.5"), header.Version()); + EXPECT_EQ(tests::Header_Version, header.Version()); EXPECT_EQ(string("unknown"), header.SortOrder()); - EXPECT_EQ(string("3.0.2"), header.PacBioBamVersion()); + EXPECT_EQ(tests::PacBioBam_Version, header.PacBioBamVersion()); EXPECT_TRUE(header.Sequences().empty()); EXPECT_TRUE(header.Comments().empty()); ASSERT_FALSE(header.Programs().empty()); diff -Nru blasr-5.3/utils/bax2bam/tests/src/test_subreads.cpp blasr-5.3+0/utils/bax2bam/tests/src/test_subreads.cpp --- blasr-5.3/utils/bax2bam/tests/src/test_subreads.cpp 2016-09-12 08:56:50.000000000 +0000 +++ blasr-5.3+0/utils/bax2bam/tests/src/test_subreads.cpp 2016-12-16 01:59:59.000000000 +0000 @@ -199,9 +199,9 @@ // check BAM header information const BamHeader& header = bamFile.Header(); - EXPECT_EQ(string("1.5"), header.Version()); + EXPECT_EQ(tests::Header_Version, header.Version()); EXPECT_EQ(string("unknown"), header.SortOrder()); - EXPECT_EQ(string("3.0.2"), header.PacBioBamVersion()); + EXPECT_EQ(tests::PacBioBam_Version, header.PacBioBamVersion()); EXPECT_TRUE(header.Sequences().empty()); EXPECT_TRUE(header.Comments().empty()); ASSERT_FALSE(header.Programs().empty());