Segmentation fault in modified_bases

[JMencius]

Hi developers of pysam, I am using the latest pysam version 0.23.3 to deal with some old PacBio data. When using read.modified_bases, the program just stop with Segmentation fault (core dumped)

Here is the ML and MM tag of the read triggers Segmentation fault occurs:

ML:B:C,254,252,255,252,254,254,255,255,252,251,254,254,253,255,251,251,253,255,255,254,252,254,255,252,254,253,252,253,255,251,251,253,254,254,251,251,254,254,251,252,252,255,251,251,253,253,254,254,255,254,252,252,253,254,251,255,253,255,251,254,254,255,253,253,252,251,252,255,251,253,251,253,254,253,253,252,251,251,254,254,251,255,255,251,253,165,90,35,198,160,149,55,55,56,100,73,212,246,252,252,249,249,239,141,123,26,75,106,229,243,242,243,205,194,78,171,163,174,254,251,250,245,109,134,151,252,250,247,251,246,223,157,82,122,169,175,172,149,74,23,19,4,9,23,212,203,221,243,227,179,111,203,190,214,219,221,147,171,141,121,220,186,63,36,6,4,1,187,179,175,130,114,246,243,242,123,159,165,158,177,103,95,152,248,225,225,230,234,208,100,13,86,145,222,234,238,240,243,249,243,213,206,127,42,49,11,17,7,4,11,9,1,1,0,0,0,0,0,3,11,54,67,48,53,115,62,44,70,97,67,48,87,172,26,33,67,89,94,6,1,6,1,0,0,0,1,10,6,5,8,7,9,39,39,74,51,28,102,160,108,11,19,6,4,0,0,0,0,0,1,7,61,156,159,244,214,199,80,28,6,4,0,0,0,4,9,12,10,99,182,224,122,121,159,44,49,5,2,1,1,0,2,2,21,58,43,29,11,7,2,1,0,0,0,1,4,6,13,19,49,48,11,10,37,24,12,6,20,29,42,42,62,93,115,247,246,244,244,250,251,252,253,254,253,245,194,180,62,208,246,250,249,255,255,233,225,159,191,190,213,204,128,167,199,226,244,236,203,224,178,189,232,132,227,252,248,251,249,221,247,244,240,247,254,253,246,246,243,242,220,250,254,254,252,252,242,242,234,235,246,244,151,126,189,176,208,210,116,161,151,79,116,104,232,240,229,237,252,246,248,250,227,248,250,249,254,253,243,225,202,186,140,68,158,91,200,177,145,156,254,254,253,254,227,214,196,247,252,245,229,246,255,248,247,250,251,255,252,230,232,213,230,144,62,200,217,249,251,245,243,253,254,254,251,228,239,243,238,234,237,250,252,254,254,251,251,252,214,222,209,101,226,242,247,247,255,255,255,255,255,255,255,255,254,253,250,241,247,251,218,240,240,236,246,246,241,241,243,242,233,238,217,221,249,249,244,248,253,253,251,250,253,242,252,254,254,254,254,255,253,253,248,212,187,216,196,80,115,85,255,254,254,254,253,254,255,251,254,254,251,252,255,255,252,252,255,254,254,251,253,254,255,253,254,255,255,253,251,255,252,251,254,255,251,253,253,254,252,254,255,254,252,252,253,253,254,253,255,255,253,254,254,254,252,253,253,251,254,254 MM:Z:A+a.,428,224,10,83,8,201,0,17,23,4,157,0,16,9,42,65,134,181,0,134,47,0,0,100,66,220,52,27,168,63,44,94,29,131,69,238,177,6,51,177,17,16,10,2,1,23,760,0,1,0,85,21,274,68,92,8,64,0,173,100,7,0,120,7,10,142,39,153,2,7,23,33,3,0,36,77,1,11,198,118,29,40,0,108,103;C+m?,35,39,60,170,82,31,6,4,1,6,18,27,30,6,18,10,7,26,7,7,10,10,15,41,17,3,31,25,2,47,126,23,7,56,6,3,68,17,8,80,70,1,5,4,7,1,3,26,6,82,20,0,12,76,27,0,6,5,50,17,10,19,41,21,25,15,5,7,4,22,61,8,15,3,12,59,58,4,35,13,2,3,56,1,20,78,5,70,6,31,33,10,54,9,12,47,13,22,23,14,6,7,10,33,0,12,42,39,15,11,2,28,2,31,9,8,19,0,16,2,28,11,29,6,9,16,1,5,13,3,11,0,4,3,1,0,7,1,5,0,2,1,1,1,1,0,1,0,1,5,0,1,6,2,0,0,3,0,1,0,1,0,0,0,0,2,0,0,0,1,0,4,2,1,0,0,0,2,0,1,1,1,1,0,0,2,0,2,1,0,2,1,3,2,4,0,1,3,2,4,0,1,0,3,1,1,0,2,3,7,0,6,4,7,3,2,2,1,9,3,4,1,3,0,0,3,5,2,6,7,0,2,3,3,2,0,3,2,1,3,7,3,1,20,16,2,16,29,5,56,12,18,77,1,31,0,13,11,0,7,9,3,8,7,1,1,2,1,32,21,11,44,27,5,3,6,2,149,70,21,30,4,1,0,2,2,2,23,10,0,1,3,51,20,37,11,8,9,16,14,21,6,26,2,9,17,37,16,43,4,41,26,23,28,5,6,1,26,8,38,14,3,0,4,1,18,25,67,10,23,2,1,10,12,4,18,2,10,6,8,1,9,10,0,2,2,4,24,3,5,10,24,7,4,43,5,8,27,21,28,34,5,0,5,9,9,17,38,6,0,6,25,4,22,30,11,2,51,0,36,0,10,6,1,2,15,3,4,3,12,8,23,9,0,1,3,7,1,14,2,13,37,4,14,43,40,24,51,8,0,9,4,8,5,0,7,0,11,39,4,1,0,23,6,0,2,17,1,1,8,9,9,68,43,3,5,6,27,8,36,35,0,6,3,4,0,16,29,36,21,0,20,6,0,3,50,5,1,8,4,4,2,4,5;T-a.,99,0,190,91,270,67,134,155,26,148,191,47,61,166,521,18,357,36,138,33,88,179,5,26,470,111,0,44,73,110,0,15,92,42,93,37,1,119,0,36,283,0,6,51,35,15,129,30,21,365,146,162,0,199,415,0,66,6,263,46;

I wonder if this have sth to do with issue #1348 or maybe you have other thoughts? Thank you for your time.

[jmarshall]

I am unable to reproduce this on macOS or Linux (both on ARM). What platform are you using? Could you attach a complete SAM file that causes the problem?

[JMencius]

Thank you for the quick response.

I am using Ubuntu on x86. below is a small BAM file I have issue to deal with.

Specifically the read with id m84039_241001_220042_s2/201785709/ccs

small.zip

[jmarshall]

Thanks. I had no problem reproducing that segfault on other platforms, though for me the problematic read was m84039_241001_220042_s2/189140546/ccs.

The problem is different from #1348, as the crash occurs in the C code, in bam_mods_at_next_pos(). That read has a fairly pointless MM tag of MM:Z:A+a.;C+m?;T-a.; and the C code doesn't handle that for reverse reads. I've reported that upstream as samtools/htslib#1936 and pysam will incorporate an eventual fix in due course.

[JMencius]

Thank you. This BAM file is not just some random dataset—it is the official PacBio Cloud-released data, available at: https://downloads.pacbcloud.com/public/revio/2024Q4/WGS/GIAB_trio/HG002_rep1/m84039_241001_220042_s2.hifi_reads.bc2018.bam and I aligned it to GRCh38 reference genome using pbmm2.

[JMencius]

Fix by samtools/htslib#1939. I’m developing a QC software with pysam. @jmarshall, may I include you in the Acknowledgements section of my paper?

[jmarshall]

Let's keep this report open to remind me to incorporate the fix into the pysam copy of the code in advance of the next release.

If getting this problem identified and fixed has been of particular use to you, I am happy to be acknowledged in your paper. Thanks!

[JMencius]

Thanks a lot, looking forward to the new version.