Add an option to skip the mate cigar in EstimateRnaSeqInsertSize #871
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nh13
commented
Aug 16, 2022
| (includeDuplicates || !rec.duplicate) && // no duplicates, unless specified | ||
| rec.mapped && rec.mateMapped && // both ends of a pair are mapped | ||
| rec.refIndex == rec.mateRefIndex && // both ends of a pair map to the same contig | ||
| (!skipMissingMateCigar || rec.mateCigar.isDefined) // skip records with missing mate cigars if specified |
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moved filters out of the old "htsjdk" filter style, so this could use a double-check
Codecov Report
@@ Coverage Diff @@
## main #871 +/- ##
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+ Coverage 95.66% 95.68% +0.02%
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Files 125 125
Lines 7239 7229 -10
Branches 507 481 -26
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- Hits 6925 6917 -8
+ Misses 314 312 -2
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NatPRoach
approved these changes
Aug 17, 2022
src/main/scala/com/fulcrumgenomics/rnaseq/EstimateRnaSeqInsertSize.scala
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…Size.scala Co-authored-by: Nathan Roach <[email protected]>
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