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support inserting RG lines

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Heng Li
2017-08-17 23:34:09 +08:00
parent b5f5929bf9
commit bbb37d95f2
5 changed files with 83 additions and 12 deletions
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minimap2.1
+8 -3
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@@ -219,13 +219,18 @@ no attempt to match GT-AG [n]
Cost of non-canonical splicing sites [0].
.SS Input/output options
.TP 10
.B -Q
Ignore base quality in the input file.
.TP
.B -a
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default.
.TP
.B -Q
Ignore base quality in the input file.
.TP
.BI -R \ STR
SAM read group line in a format like
.B @RG\\\\tID:foo\\\\tSM:bar
[].
.TP
.B -c
Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
.TP