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Released bwa-0.7.4-r385

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Heng Li 2013-04-23 11:40:56 -04:00
parent 2f6897c72b
commit c14aaad1ce
2 changed files with 21 additions and 18 deletions
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37
bwa.1
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.TH bwa 1 "15 March 2013" "bwa-0.7.4" "Bioinformatics tools" .TH bwa 1 "23 April 2013" "bwa-0.7.4" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
bwa - Burrows-Wheeler Alignment Tool bwa - Burrows-Wheeler Alignment Tool
@ -44,7 +44,12 @@ for the BWA-MEM algorithm.
.SH COMMANDS AND OPTIONS .SH COMMANDS AND OPTIONS
.TP .TP
.B index .B index
bwa index [-p prefix] [-a algoType] <in.db.fasta> .B bwa index
.RB [ -p
.IR prefix ]
.RB [ -a
.IR algoType ]
.I db.fa
Index database sequences in the FASTA format. Index database sequences in the FASTA format.
@ -55,20 +60,16 @@ Index database sequences in the FASTA format.
Prefix of the output database [same as db filename] Prefix of the output database [same as db filename]
.TP .TP
.BI -a \ STR .BI -a \ STR
Algorithm for constructing BWT index. Available options are: Algorithm for constructing BWT index. BWA implements two algorithms for BWT
.RS construction:
.TP
.B is .B is
IS linear-time algorithm for constructing suffix array. It requires and
5.37N memory where N is the size of the database. IS is moderately fast, .BR bwtsw .
but does not work with database larger than 2GB. IS is the default The first algorithm is a little faster for small database but requires large
algorithm due to its simplicity. The current codes for IS algorithm are RAM and does not work for databases with total length longer than 2GB. The
reimplemented by Yuta Mori. second algorithm is adapted from the BWT-SW source code. It in theory works
.TP with database with trillions of bases. When this option is not specified, the
.B bwtsw appropriate algorithm will be chosen automatically.
Algorithm implemented in BWT-SW. This method works with the whole human
genome.
.RE
.RE .RE
.TP .TP
@ -220,10 +221,12 @@ deducted. [5]
Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
.RI scoreRead1+scoreRead2- INT .RI scoreRead1+scoreRead2- INT
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. [17] two scores to determine whether we should force pairing. A larger value leads to
more aggressive read pair. [17]
.TP .TP
.B -p .B -p
Assume the first input query file is interleaved paired-end FASTA/Q. See the command description for details. Assume the first input query file is interleaved paired-end FASTA/Q. See the
command description for details.
.TP .TP
.BI -R \ STR .BI -R \ STR
Complete read group header line. '\\t' can be used in Complete read group header line. '\\t' can be used in

2
main.c
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#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r384-beta" #define PACKAGE_VERSION "0.7.4-r385"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);