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Typos, doc improvements in man page #60

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Jul 30, 2017
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Typos, doc improvements in man page #60

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e10fc57
Fix a few typos in man page
jdagilliland Mar 31, 2016
d6636da
Include in man page info on read types
jdagilliland Mar 31, 2016
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18 changes: 16 additions & 2 deletions bwa.1
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,8 @@ appropriate algorithm will be chosen automatically.
.IR clipPen ]
.RB [ -U
.IR unpairPen ]
.RB [ -x
.IR readType ]
.RB [ -R
.IR RGline ]
.RB [ -H
Expand Down Expand Up @@ -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
two scores to determine whether we should force pairing. A larger value leads to
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
.B INPUT/OUTPUT OPTIONS:
Expand Down Expand Up @@ -302,7 +316,7 @@ Output all found alignments for single-end or unpaired paired-end reads. These
alignments will be flagged as secondary alignments.
.TP
.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
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.
Expand All @@ -316,7 +330,7 @@ supplementary alignments.
Mark shorter split hits as secondary (for Picard compatibility).
.TP
.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
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
Expand Down
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