Merge branch 'master' into master_fixes. Merged up to release bwa-0.7.4-r385.
This commit is contained in:
Rob Davies
commit
b3d0a13b32
2
Makefile
2
Makefile
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@ -7,7 +7,7 @@ AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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is.o bwtindex.o bwape.o kopen.o pemerge.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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PROG= bwa bwamem-lite
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PROG= bwa
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INCLUDES=
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LIBS= -lm -lz -lpthread
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SUBDIRS= .
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33
NEWS
33
NEWS
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@ -1,3 +1,36 @@
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Release 0.7.4 (23 April, 2013)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is a bugfix release. Most of bugs are considered to be minor which only
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very rarely.
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ccur
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* Bugfix: wrong CIGAR when a query sequence bridges three or more target
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sequences. This only happens when aligning reads to short assembly contigs.
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* Bugfix: leading "D" operator in CIGAR.
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* Extend more seeds for better alignment around tandem repeats. This is also
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a cause of the leading "D" operator in CIGAR.
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* Bugfix: SSE2-SSW may occasionally find incorrect query starting position
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around tandem repeat. This will lead to a suboptimal CIGAR in BWA-MEM and
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a wrong CIGAR in BWA.
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* Bugfix: clipping penalty does not work as is intended when there is a gap
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towards the end of a read.
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* Fixed an issue caused by a bug in the libc from Mac/Darwin. In Darwin,
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fread() is unable to read a data block longer than 2GB due to an integer
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overflow bug in its implementation.
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Since version 0.7.4, BWA-MEM is considered to reach similar stability to
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BWA-backtrack for short-read mapping.
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(0.7.4: 23 April, r385)
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Release 0.7.3a (15 March, 2013)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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37
bwa.1
37
bwa.1
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@ -1,4 +1,4 @@
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.TH bwa 1 "15 March 2013" "bwa-0.7.4" "Bioinformatics tools"
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.TH bwa 1 "23 April 2013" "bwa-0.7.4" "Bioinformatics tools"
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.SH NAME
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.PP
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bwa - Burrows-Wheeler Alignment Tool
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@ -44,7 +44,12 @@ for the BWA-MEM algorithm.
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.SH COMMANDS AND OPTIONS
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.TP
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.B index
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bwa index [-p prefix] [-a algoType] <in.db.fasta>
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.B bwa index
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.RB [ -p
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.IR prefix ]
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.RB [ -a
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.IR algoType ]
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.I db.fa
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Index database sequences in the FASTA format.
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@ -55,20 +60,16 @@ Index database sequences in the FASTA format.
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Prefix of the output database [same as db filename]
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.TP
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.BI -a \ STR
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Algorithm for constructing BWT index. Available options are:
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.RS
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.TP
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Algorithm for constructing BWT index. BWA implements two algorithms for BWT
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construction:
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.B is
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IS linear-time algorithm for constructing suffix array. It requires
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5.37N memory where N is the size of the database. IS is moderately fast,
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but does not work with database larger than 2GB. IS is the default
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algorithm due to its simplicity. The current codes for IS algorithm are
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reimplemented by Yuta Mori.
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.TP
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.B bwtsw
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Algorithm implemented in BWT-SW. This method works with the whole human
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genome.
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.RE
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and
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.BR bwtsw .
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The first algorithm is a little faster for small database but requires large
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RAM and does not work for databases with total length longer than 2GB. The
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second algorithm is adapted from the BWT-SW source code. It in theory works
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with database with trillions of bases. When this option is not specified, the
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appropriate algorithm will be chosen automatically.
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.RE
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.TP
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@ -220,10 +221,12 @@ deducted. [5]
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Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
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.RI scoreRead1+scoreRead2- INT
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and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these
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two scores to determine whether we should force pairing. [17]
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two scores to determine whether we should force pairing. A larger value leads to
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more aggressive read pair. [17]
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.TP
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.B -p
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Assume the first input query file is interleaved paired-end FASTA/Q. See the command description for details.
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Assume the first input query file is interleaved paired-end FASTA/Q. See the
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command description for details.
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.TP
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.BI -R \ STR
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Complete read group header line. '\\t' can be used in
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6
main.c
6
main.c
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@ -3,7 +3,7 @@
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#include "utils.h"
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#ifndef PACKAGE_VERSION
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#define PACKAGE_VERSION "0.7.3-r382-beta"
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#define PACKAGE_VERSION "0.7.4-r385"
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#endif
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int bwa_fa2pac(int argc, char *argv[]);
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@ -46,6 +46,10 @@ static int usage()
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fprintf(stderr, " bwtupdate update .bwt to the new format\n");
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fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
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fprintf(stderr, "\n");
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fprintf(stderr, "Note: To use BWA, you need to first index the genome with `bwa index'. There are\n");
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fprintf(stderr, " three alignment algorithms in BWA: `mem', `bwasw' and `aln/samse/sampe'. If\n");
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fprintf(stderr, " you are not sure which to use, try `bwa mem' first. Please `man ./bwa.1' for\n");
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fprintf(stderr, " for the manual.\n\n");
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return 1;
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}
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