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Document --no-pairing (#256)

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Heng Li 2018-10-23 10:00:21 -04:00
parent 377c7099a8
commit ecb6c5c36c
1 changed files with 4 additions and 0 deletions
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@ -274,6 +274,10 @@ Only map to the reverse complement strand of the reference sequences.
.BR --heap-sort = no | yes .BR --heap-sort = no | yes
If yes, sort anchors with heap merge, instead of radix sort. Heap merge is If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
faster for short reads, but slower for long reads. [no] faster for short reads, but slower for long reads. [no]
.TP
.B --no-pairing
Treat two reads in a pair as independent reads. The mate related fields in SAM
are still properly populated.
.SS Alignment options .SS Alignment options
.TP 10 .TP 10
.BI -A \ INT .BI -A \ INT