Sambamba with htslib 1.10.2 #425
Description
Dear,
Thanks for your awesome project.
We are trying to build sambamba version 0.7.1 whith htslib 1.10.2 provided by samtools.
Thus we have use patched:
htslib/cram/cram_decode.handhtslib/cram/cram_decode.cfrom htslib- Makefile in order to link to needed library
curl,liblxzmaandlibbzip2 cram/htslib.dfrom sambamba in order to not use deprecated symbolcram/writer.dfrom sambamba in order to not use deprecated symbol
The build works fine but test about cram fail:
sambamba-0.7.1: ./run_tests.sh bin/sambamba-0.7.1
sambamba-0.7.1: Running tests for bin/sambamba-0.7.1...
sambamba-0.7.1: #
sambamba-0.7.1: # Performing tests
sambamba-0.7.1: #
sambamba-0.7.1: testSamtoBam
sambamba-0.7.1: testSubSample
sambamba-0.7.1: testSortByName
sambamba-0.7.1: testSortByCoordinate
sambamba-0.7.1: testSortPicard
sambamba-0.7.1: testSortByNameMatchMates
sambamba-0.7.1: testNaturalSortMatchMates
sambamba-0.7.1: testSlice
sambamba-0.7.1: testSliceMultipleRegions
sambamba-0.7.1: testSliceMultipleRegionsBed
sambamba-0.7.1: ASSERT:expected:<156> but was:<0>
sambamba-0.7.1: testView
sambamba-0.7.1: testOverwriteProtection
sambamba-0.7.1: testSortingEmptyFile
sambamba-0.7.1: testMarkdupEmptyFile
sambamba-0.7.1: testCramWriting
sambamba-0.7.1: [E::cram_get_ref] No reference found for id 67113545
sambamba-0.7.1: [E::cram_encode_container] Failed to load reference #67113545
sambamba-0.7.1: [E::cram_flush_thread] Call to cram_encode_container failed
sambamba-0.7.1: [E::cram_get_ref] No reference found for id 67113545
sambamba-0.7.1: [E::cram_encode_container] Failed to load reference #67113545
sambamba-0.7.1: [E::cram_flush_thread] Call to cram_encode_container failed
sambamba-0.7.1: ./test/test_suite.sh: line 143: 27561 Segmentation fault (core dumped) $sambamba $opts view -S htslib/test/c1#pad2.sam -T htslib/test/c1.fa -f cram -o $outdir/c1_pad2.cram
sambamba-0.7.1: ASSERT:expected:<0> but was:<139>
sambamba-0.7.1: testCramReading
sambamba-0.7.1: ./test/test_suite.sh: line 148: 27680 Segmentation fault (core dumped) $sambamba $opts view -C $outdir/c1_pad2.cram > /dev/null
sambamba-0.7.1: ASSERT:expected:<0> but was:<139>
sambamba-0.7.1: testIndexUsage
sambamba-0.7.1: [E::cram_get_ref] No reference found for id 67113545
sambamba-0.7.1: [E::cram_encode_container] Failed to load reference #67113545
sambamba-0.7.1: [E::cram_flush_thread] Call to cram_encode_container failed
Thanks for you help
Have a nice day
sambamba-0.7.1-fix_htslib_func_call.txt