[Debian-med-packaging] Bug#829741: pbbam: FTBFS (32-bit): pbmerge assertion failure

[Aaron M. Ucko]

Source: pbbam
Version: 0.5.0-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Builds of pbbam for 32-bit architectures such as i386 fail because
pbmerge hits an assertion failure in the context of the
pbmerge_aligned_ordering and pbmerge_fofn tests, per the excerpted log
output below.  Could you please take a look?

Thanks!

  TESTDIR=tests/src/cram cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_dataset.deb.t
  tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed
  tests/src/cram/pbmerge_mixed_ordering.deb.t: passed
  tests/src/cram/pbmerge_aligned_ordering.deb.t: failed
  --- tests/src/cram/pbmerge_aligned_ordering.deb.t
  +++ tests/src/cram/pbmerge_aligned_ordering.deb.t.err
  @@ -122,35 +122,13 @@
   Explicit Output Filename (also enables PBI):
   
     $ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2
  +  pbmerge: /«PKGBUILDDIR»/src/PbiBuilder.cpp:322: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed.
  +  Aborted
  +  [134]
   
     $ samtools view -H $MERGED_BAM
  -  @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
  -  @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
  -  @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
  -  @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-0.5.0\tPN:pbmerge\tVN:0.5.0 (esc)
   
     $ samtools view  $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)
  -  m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc)
  [...]
  -  m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc)
   
     $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
     Found
  tests/src/cram/pbindexdump_json.deb.t: passed
  tests/src/cram/pbindexdump_cpp.deb.t: passed
  tests/src/cram/pbmerge_fofn.deb.t: failed
  --- tests/src/cram/pbmerge_fofn.deb.t
  +++ tests/src/cram/pbmerge_fofn.deb.t.err
  @@ -53,6 +53,9 @@
   Normal Merge from FOFN:
   
     $ $PBMERGE -o $MERGED_BAM $INPUT_FOFN
  +  pbmerge: /«PKGBUILDDIR»/src/PbiBuilder.cpp:322: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed.
  +  Aborted
  +  [134]
   
     $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found"
     Found
  @@ -61,33 +64,8 @@
     Found
   
     $ samtools view -H $MERGED_BAM
  -  @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
  -  @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
  -  @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
  -  @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-0.5.0\tPN:pbmerge\tVN:0.5.0 (esc)
   
     $ samtools view  $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)
  -  m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc)
  [...]
  -  m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc)
   
     $ rm $MERGED_BAM
     $ rm $MERGED_BAM_PBI
  tests/src/cram/pbmerge_dataset.deb.t: passed
  # Ran 7 tests, 0 skipped, 2 failed.
  debian/rules:25: recipe for target 'override_dh_auto_test' failed
  make[1]: *** [override_dh_auto_test] Error 1
  make[1]: Leaving directory '/«PKGBUILDDIR»'
  debian/rules:10: recipe for target 'build-arch' failed
  make: *** [build-arch] Error 2
  dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2