Andreas Tille pushed to branch master at Debian Med / pbbam
Commits: 3d9ec593 by Andreas Tille at 2018-10-03T19:49:15Z Add some debug code to track down #909071 (no solution yet - any volunteer?) - - - - - a2e34721 by Andreas Tille at 2018-10-03T19:57:05Z Add Breaks+Provides+Replaces - - - - - 231ef337 by Andreas Tille at 2018-10-03T19:59:10Z Missing Breaks+Replaces: libpbbam (<< 0.18) - - - - - a13006ae by Andreas Tille at 2018-10-03T20:24:36Z No needs-recommends restrictions, just Test-Depends: samtools - - - - - a90e83c9 by Andreas Tille at 2018-10-03T20:36:34Z Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/debug_tests.patch - debian/patches/series - debian/rules - debian/tests/control Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +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 <[email protected]> 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 ===================================== @@ -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 ===================================== @@ -0,0 +1,97 @@ +Description: Only debug code to track down bug #909071 i386 (no solution yet) +Bug-Debian: https://bugs.debian.org/909071 +Author: Andreas Tille <[email protected]> +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 $MERGED_BAM | cut -f 1,3,4 | head -n 20 + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ fix_gtest_depcheck.patch +# debug_tests.patch ===================================== debian/rules ===================================== @@ -34,7 +34,7 @@ ifeq (,$(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 ===================================== @@ -4,6 +4,6 @@ Depends: python, pbbamtools, python-cram, + samtools Restrictions: - needs-recommends, rw-build-tree, View it on GitLab: https://salsa.debian.org/med-team/pbbam/compare/bebb30604c1b1cd2fec217641e835e68f4ec453f...a90e83c9fdcbcd2415303185465e50926c78680e -- View it on GitLab: https://salsa.debian.org/med-team/pbbam/compare/bebb30604c1b1cd2fec217641e835e68f4ec453f...a90e83c9fdcbcd2415303185465e50926c78680e You're receiving this email because of your account on salsa.debian.org.
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