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r340: feature freeze; updated the manpage 

I will stop adding new features to bwa and prepare for the next release. I will
briefly evaluate the variant calling accuracy before the release.
This commit is contained in:
Heng Li 2013-03-07 11:51:23 -05:00
parent 503ca9ed2e
commit b0a76884e8
3 changed files with 26 additions and 4 deletions
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24
bwa.1
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@ -1,4 +1,4 @@
.TH bwa 1 "27 Feburary 2013" "bwa-0.7.0" "Bioinformatics tools"
.TH bwa 1 "10 March 2013" "bwa-0.7.1" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
@ -81,6 +81,8 @@ genome.
.IR minSeedLen ]
.RB [ -w
.IR bandWidth ]
.RB [ -d
.IR zDropoff ]
.RB [ -r
.IR seedSplitRatio ]
.RB [ -c
@ -163,6 +165,21 @@ Band width. Essentially, gaps longer than
will not be found. Note that the maximum gap length is also affected by the
scoring matrix and the hit length, not solely determined by this option. [100]
.TP
.BI -d \ INT
Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between
the best and the current extension score is above
.RI | i - j |* A + INT ,
where
.I i
and
.I j
are the current positions of the query and reference, respectively, and
.I A
is the matching score. Z-dropoff is similar to BLAST's X-dropoff except that it
doesn't penalize gaps in one of the sequences in the alignment. Z-dropoff not
only avoids unnecessary extension, but also reduces poor alignments inside a
long good alignment. [100]
.TP
.BI -r \ FLOAT
Trigger re-seeding for a MEM longer than
.IR minSeedLen * FLOAT .
@ -215,6 +232,11 @@ and will be converted to a TAB in the output SAM. The read group ID will be
attached to every read in the output. An example is '@RG\\tID:foo\\tSM:bar'.
[null]
.TP
.BI -T \ INT
Don't output alignment with score lower than
.IR INT .
This option only affects output. [30]
.TP
.B -a
Output all found alignments for single-end or unpaired paired-end reads. These
alignments will be flagged as secondary alignments.

2
fastmap.c
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@ -59,7 +59,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -k INT minimum seed length [%d]\n", opt->min_seed_len);
fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w);
fprintf(stderr, " -d INT off-diagnal X-dropoff [%d]\n", opt->zdrop);
fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop);
fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
// fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ);

4
main.c
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@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.0-r339-beta"
#define PACKAGE_VERSION "0.7.0-r340-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);
@ -34,7 +34,7 @@ static int usage()
fprintf(stderr, "Command: index index sequences in the FASTA format\n");
fprintf(stderr, " mem BWA-MEM algorithm\n");
fprintf(stderr, " fastmap identify super-maximal exact matches\n");
fprintf(stderr, " pemerge merge overlapping paired ends\n");
fprintf(stderr, " pemerge merge overlapping paired ends (EXPERIMENTAL)\n");
fprintf(stderr, " aln gapped/ungapped alignment\n");
fprintf(stderr, " samse generate alignment (single ended)\n");
fprintf(stderr, " sampe generate alignment (paired ended)\n");