Emit M instead of =/X CIGAR operations by default #261
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Great! And I agree that we should change default to be M and have the flag I will restart the SNV/indel calling benchmark once this is merged. |
marcelm
changed the title
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Alright, updated to use |
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The evaluation of this commit was posted here: #245 (comment) |
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I needed to do some refactoring so that CIGARs are internally always represented as
Cigarobjects and only converted to their string representation at the very last moment when the alignments are serialized to SAM format. This makes it easy to optionally convert them to useMinstead of=/Xoperations since the logic for that needs to be in only one place.I chose
--m-opas the name for the command-line option for now, but I’m not super happy with it. Bowtie2 and minimap2 have an--eqxswitch and the opposite behavior:Mby default and=/Xis optional. Perhaps we should change the default as well for better compatibility? Also, that would avoid the spurious variant calling issue as long as htslib is not fixed.