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Include in man page info on read types 

Previously this info had only been present in the help text emitted from
`bwa mem` without arguments, but I think it helpful to include in man page.
This commit is contained in:
Jason Gilliland 2016-03-31 12:39:24 -04:00
parent e10fc577e1
commit d6636daead
1 changed files with 14 additions and 0 deletions
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@ -107,6 +107,8 @@ appropriate algorithm will be chosen automatically.
.IR clipPen ] .IR clipPen ]
.RB [ -U .RB [ -U
.IR unpairPen ] .IR unpairPen ]
.RB [ -x
.IR readType ]
.RB [ -R .RB [ -R
.IR RGline ] .IR RGline ]
.RB [ -H .RB [ -H
@ -256,6 +258,18 @@ Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these
two scores to determine whether we should force pairing. A larger value leads to two scores to determine whether we should force pairing. A larger value leads to
more aggressive read pair. [17] more aggressive read pair. [17]
.TP
.BI -x \ STR
Read type. Changes multiple parameters unless overriden [null]
pacbio:
.B -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0
(PacBio reads to ref)
ont2d:
.B -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0
(Oxford Nanopore 2D-reads to ref)
intractg:
.B -B9 -O16 -L5
(intra-species contigs to ref)
.TP .TP
.B INPUT/OUTPUT OPTIONS: .B INPUT/OUTPUT OPTIONS: