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Reenable samtools read count cross checks in HtsjdkReadsRddTest.testReadIntervals #163

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cmnbroad opened this issue Jan 31, 2022 · 0 comments
Open

Reenable samtools read count cross checks in HtsjdkReadsRddTest.testReadIntervals #163

cmnbroad opened this issue Jan 31, 2022 · 0 comments

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@cmnbroad
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cmnbroad commented Jan 31, 2022 •
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HtsjdkReadsRddTest.testReadIntervals cross checks its output by verifying that the read counts as returned by htsjdk and samtools are the same. Samtools/htslib have a bug (samtools/htslib#1387) that can return incorrect read counts for unmapped reads, so this checking is disabled by #164. When a version of samtools with a fix for that issue is released, we should upgrade disq to use the new version and reenable the cross checks.
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