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debian/changelog
View file @ a90e83c9
pbbam (0.18.0+dfsg-2) unstable; urgency=medium
* Team upload.
* Missing Breaks+Replaces: libpbbam (<< 0.18)
Closes: #910206
* No needs-recommends restrictions, just Test-Depends: samtools
-- Andreas Tille <tille@debian.org> Wed, 03 Oct 2018 22:24:56 +0200
pbbam (0.18.0+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
......@@ -12,6 +21,7 @@ pbbam (0.18.0+dfsg-1) unstable; urgency=medium
* Remove unneeded trigger
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test
* hardening=+all
* Add Breaks/Provides/Replaces libpbbam
[ Fabian Kloetzl ]
* fix dependency check for meson
......
debian/control
View file @ a90e83c9
......@@ -48,6 +48,9 @@ Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
Breaks: libpbbam (<< ${source:Version})
Provides: libpbbam
Replaces: libpbbam
Pre-Depends: ${misc:Pre-Depends}
Description: Pacific Biosciences binary alignment/map (BAM) library
The BAM format is a binary, compressed, record-oriented container format
......@@ -67,6 +70,8 @@ Depends: libpbbam0.18.0 (= ${binary:Version}),
libhts-dev,
libssl-dev,
${misc:Depends}
Breaks: libpbbam (<< 0.18)
Replaces: libpbbam (<< 0.18)
Description: Pacific Biosciences binary alignment/map (BAM) library (headers)
The BAM format is a binary, compressed, record-oriented container format
for raw or aligned sequence reads. The associated SAM format is a text
......
debian/patches/debug_tests.patch 0 → 100644
View file @ a90e83c9
Description: Only debug code to track down bug #909071 i386 (no solution yet)
Bug-Debian: https://bugs.debian.org/909071
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 18 Sep 2018 08:40:19 +0200
--- a/tests/src/cram/pbmerge_pacbio_ordering.t.in
+++ b/tests/src/cram/pbmerge_pacbio_ordering.t.in
@@ -13,6 +13,8 @@ Setup:
Sanity Check:
+ $ ls -l $HQREGION_BAM
+ $ echo "DEBUG: $BAM2SAM --header-only $HQREGION_BAM"
$ $BAM2SAM --header-only $HQREGION_BAM
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
@@ -20,9 +22,11 @@ Sanity Check:
@PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc)
@PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc)
+ $ echo "DEBUG: $BAM2SAM --no-header $HQREGION_BAM | cut -f 1"
$ $BAM2SAM --no-header $HQREGION_BAM | cut -f 1
ArminsFakeMovie/100000/2659_7034
+ $ $echo "DEBUG: BAM2SAM --header-only $SCRAPS_BAM"
$ $BAM2SAM --header-only $SCRAPS_BAM
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
@@ -30,6 +34,7 @@ Sanity Check:
@PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc)
@PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc)
+ $ echo "DEBUG: $BAM2SAM --no-header $SCRAPS_BAM | cut -f 1"
$ $BAM2SAM --no-header $SCRAPS_BAM | cut -f 1
ArminsFakeMovie/100000/0_2659
ArminsFakeMovie/100000/3025_3047
--- a/tests/src/cram/pbmerge_aligned_ordering.t.in
+++ b/tests/src/cram/pbmerge_aligned_ordering.t.in
@@ -51,7 +51,10 @@ Sanity Check:
Normal Merge:
+ $ echo "DEBUG: $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM"
$ $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM
+ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 1: File $MERGED_BAM does not exists - no idea why. Try again creating it after 5s."; $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ; fi
+ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 1: File $MERGED_BAM does not exists - even after trying again."; exit ; else echo echo "File $MERGED_BAM was created now" ; fi
$ $BAM2SAM --header-only $MERGED_BAM
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@@ -60,6 +63,7 @@ Normal Merge:
@PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
@PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
+ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
$ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
@@ -86,8 +90,15 @@ Normal Merge:
Shuffle Input:
+ $ echo DEBUG: PATH = $PATH
+ $ which pbmerge
+ $ echo "DEBUG: $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM"
$ $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM
+ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 2: File $MERGED_BAM does not exists - no idea why. Try again creating it after 5s."; $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ; fi
+ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 2: File $MERGED_BAM does not exists - even after trying again."; exit ; else echo echo "File $MERGED_BAM was created now" ; fi
+ $ echo "DEBUG: $BAM2SAM --header-only $MERGED_BAM"
+ $ echo "DEBUG: That is the problematic command"
$ $BAM2SAM --header-only $MERGED_BAM
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@@ -95,6 +106,7 @@ Shuffle Input:
@PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
@PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
+ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
$ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
@@ -130,6 +142,7 @@ Explicit Output Filename (also enables P
@PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
@PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
+ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
$ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
@@ -169,6 +182,7 @@ Explicit Output Filename (with disabled
@PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
@PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
+ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
$ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
debian/patches/series
View file @ a90e83c9
fix_gtest_depcheck.patch
# debug_tests.patch
debian/rules
View file @ a90e83c9
......@@ -34,7 +34,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
BINDIR=`dirname $$(find $$PWD -name pbmerge -type f -executable)`; \
LIBDIR=`find $$PWD -name lib -type d`; \
PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \
cram -v $^
cram -v --preserve-env $^
endif
override_dh_installchangelogs:
......
debian/tests/control
View file @ a90e83c9
......@@ -4,6 +4,6 @@ Depends:
python,
pbbamtools,
python-cram,
samtools
Restrictions:
needs-recommends,
rw-build-tree,