Change default sort orders of consensus callers #781
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This affects CallDuplexConsensusReads and CallMolecularConsensusReads. When no sort order is given, the output is unsorted but query-grouped, which is sufficient for either downstream re-alignment or consensus filtering. We can thus avoid sorting the output consensus reads when calling.
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## master #781 +/- ##
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- Coverage 95.47% 95.47% -0.01%
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Files 121 121
Lines 6852 6874 +22
Branches 461 464 +3
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nh13
commented
Feb 26, 2022
src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala
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src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala
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tfenne
approved these changes
Feb 26, 2022
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This affects CallDuplexConsensusReads and CallMolecularConsensusReads.
When no sort order is given, the output is unsorted but query-grouped,
which is sufficient for either downstream re-alignment or consensus
filtering. We can thus avoid sorting the output consensus reads when
calling.
I think
picard MergeBamAlignmentwill not like this, as it wantsqueryname, notunsorted:querygrouped, so leaving this as a draft for now.