[med-svn] [Git][med-team/pbbam][master] 5 commits: Add some debug code to track down #909071 (no solution yet - any volunteer?)
Andreas Tille
gitlab at salsa.debian.org
Wed Oct 3 21:37:15 BST 2018
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 <tille at 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
=====================================
@@ -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 <tille at 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- at 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- at 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- at 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- at 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
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