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Disable fixmate test (for now) due to behaviour change
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From the SAMtools v1.21 release notes: `samtools fixmate` no longer
removes the PAIRED flag from reads that have no mate. This is done
on the understanding that the PAIRED flag is a sequencing technology
indicator not a feature of alignment.
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jmarshall committed Oct 3, 2024
1 parent 0ad4778 commit 6147f5d
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion tests/samtools_test.py
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,8 @@ class SamtoolsTest(unittest.TestCase):
"index ex1.bam %(out)s_ex1.bam.fai",
"index -@2 ex1.bam %(out)s_ex1.bam.fai",
"idxstats ex1.bam > %(out)s_ex1.idxstats",
"fixmate ex1.bam %(out)s_ex1.fixmate.bam",
# TODO: fixmate behaviour changed in 1.21
#"fixmate ex1.bam %(out)s_ex1.fixmate.bam",
"flagstat ex1.bam > %(out)s_ex1.flagstat",
"calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
# use -s option, otherwise the following error in samtools 1.2:
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