mpileup-1.16.patch: add; fix mpileup calls since htslib 1.16.
Closes: #1021675, #1022508
Étienne Mollier
1 year, 5 months ago
| 0 | Description: move to bcftools 1.16 mpileup | |
| 1 | The original mpileup command from samtools has been deprecated and removed | |
| 2 | starting with version 1.16. The command has been moved to bcftools 1.16. | |
| 3 | This patch adjusts the pysam call to reach for bcftools appropriately instead | |
| 4 | of the plain samtools wrapper. | |
| 5 | Author: Étienne Mollier <emollier@debian.org> | |
| 6 | Bug: https://github.com/sanger-pathogens/ariba/issues/327 | |
| 7 | Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022508 | |
| 8 | Last-Update: 2022-11-28 | |
| 9 | --- | |
| 10 | This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ | |
| 11 | --- ariba.orig/ariba/samtools_variants.py | |
| 12 | +++ ariba/ariba/samtools_variants.py | |
| 13 | @@ -1,6 +1,7 @@ | |
| 14 | import os | |
| 15 | import sys | |
| 16 | import pysam | |
| 17 | +import pysam.bcftools | |
| 18 | import pyfastaq | |
| 19 | import vcfcall_ariba | |
| 20 | ||
| 21 | @@ -36,13 +37,11 @@ | |
| 22 | ||
| 23 | tmp_vcf = self.vcf_file + '.tmp' | |
| 24 | with open(tmp_vcf, 'w') as f: | |
| 25 | - print(pysam.mpileup( | |
| 26 | + print(pysam.bcftools.mpileup( | |
| 27 | '-t', 'INFO/AD,INFO/ADF,INFO/ADR', | |
| 28 | '-L', '99999999', | |
| 29 | '-A', | |
| 30 | '-f', self.ref_fa, | |
| 31 | - '-u', | |
| 32 | - '-v', | |
| 33 | self.bam, | |
| 34 | ), end='', file=f) | |
| 35 |