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Merge pull request #60 from jdagilliland/typo 

Typos, doc improvements in man page
This commit is contained in:
Heng Li 2017-07-30 18:59:11 -04:00 committed by GitHub
parent 1eee77ad93 d6636daead
commit 83260ccb10
1 changed files with 16 additions and 2 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:
@ -310,7 +324,7 @@ Output all found alignments for single-end or unpaired paired-end reads. These
alignments will be flagged as secondary alignments. alignments will be flagged as secondary alignments.
.TP .TP
.B -C .B -C
Append append FASTA/Q comment to SAM output. This option can be used to Append FASTA/Q comment to SAM output. This option can be used to
transfer read meta information (e.g. barcode) to the SAM output. Note that the transfer read meta information (e.g. barcode) to the SAM output. Note that the
FASTA/Q comment (the string after a space in the header line) must conform the SAM FASTA/Q comment (the string after a space in the header line) must conform the SAM
spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output. spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
@ -324,7 +338,7 @@ supplementary alignments.
Mark shorter split hits as secondary (for Picard compatibility). Mark shorter split hits as secondary (for Picard compatibility).
.TP .TP
.BI -v \ INT .BI -v \ INT
Control the verbose level of the output. This option has not been fully Control the verbosity level of the output. This option has not been fully
supported throughout BWA. Ideally, a value 0 for disabling all the output to supported throughout BWA. Ideally, a value 0 for disabling all the output to
stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for
all normal messages; 4 or higher for debugging. When this option takes value all normal messages; 4 or higher for debugging. When this option takes value