Closed SoapGentoo closed 3 months ago
If you avoid capturing the output, you will see that this is preceded by an error message from htslib:
[E::bam_parse_basemod2] *: Too many entries in ML tag
This data file contains invalid data, which is diagnosed by improvements in bam_parse_basemod2()
in HTSlib 1.20. Updating these base modification data files to the versions in htslib and hts-specs corrects the problem.
Thanks for the report. If you want a minimal patch to apply to correct this test case, it would be
diff --git a/tests/pysam_data/MM-chebi.sam b/tests/pysam_data/MM-chebi.sam
index 62920ec..28774d5 100644
--- a/tests/pysam_data/MM-chebi.sam
+++ b/tests/pysam_data/MM-chebi.sam
@@ -1,2 +1,2 @@
@CO Separate m, h and N modifications
-* 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15; Ml:B:C,102,128,153,179,204,161,187,212,169
+* 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15; Ml:B:C,102,128,153,179,204,161,187,212
I'm trying to package pysam 0.22.1 with htslib 1.20 (so we can get rid of 1.18 in our repo) and have run into one base modifications failure: