dalexander / pysam_issue

htslib problem in version bundled with pysam-0.8.0

This is a problem with htslib, not pysam. The problem a bug in bgzf_tell or bgzf_seek, apparently fixed here:

https://github.com/samtools/htslib/commit/c99ed6aa47b5af768053bc6de895d284a440638f

The bug is apparent on running the following command and looking at the first output, the result of tell following a seek.

$ pysam_example.py bam_mapping.bam

pysam 0.8.0 “off the shelf” (incorrect output, note result of first tell):

$ ./pysam_example.py bam_mapping.bam
0x25700000000      m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/47698/10378_10609
0x2570709          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/47698/9675_10333
0x2571951          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/47698/9482_9628
0x2571e03          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49194/845_1541
0x25731dc          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49194/0_798
0x25748c6          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134
0x2575e1b          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344
0x2576822          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132
0x2578695          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/15641/3452_3567

pysam 0.8.0, linked against htslib 1.1: (correct output):

$ ./pysam_example.py bam_mapping.bam
0x2570000          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/47698/10378_10609
0x2570709          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/47698/9675_10333
0x2571951          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/47698/9482_9628
0x2571e03          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49194/845_1541
0x25731dc          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49194/0_798
0x25748c6          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134
0x2575e1b          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344
0x2576822          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132
0x2578695          m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/15641/3452_3567