Commit 147c5782 authored by Charles Plessy's avatar Charles Plessy

Merge commit 'upstream/0.5.5'

parents 57c46a98 f2bef380
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Beta Release 0.5.5 (10 November, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is a bug fix release:
* Fixed a serious bug/typo in aln which does not occur given short
reads, but will lead to segfault for >500bp reads. Of course, the aln
command is not recommended for reads longer than 200bp, but this is a
bug anyway.
* Fixed a minor bug/typo which leads to incorrect single-end mapping
quality when one end is moved to meet the mate-pair requirement.
* Fixed a bug in samse for mapping in the color space. This bug is
caused by quality filtration added since 0.5.1.
(0.5.5: 10 November 2009, r1273)
Beta Release 0.5.4 (9 October, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
.TH bwa 1 "9 October 2009" "bwa-0.5.4" "Bioinformatics tools"
.TH bwa 1 "10 November 2009" "bwa-0.5.5" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
......
......@@ -417,4 +417,4 @@ HISTORY
bwa-0.5.4 9 October 2009 bwa(1)
bwa-0.5.5 10 November 2009 bwa(1)
......@@ -211,7 +211,7 @@ static int pairing(bwa_seq_t *p[2], pe_data_t *d, const pe_opt_t *opt, int s_mm,
p[1]->seQ = 0; p[1]->mapQ = p[0]->mapQ;
if (p[1]->mapQ > mapQ_p) p[1]->mapQ = mapQ_p;
} else if (p[1]->pos == o_pos[1]>>32) { // [0] moved
p[1]->seQ = 0; p[0]->mapQ = p[1]->mapQ;
p[0]->seQ = 0; p[0]->mapQ = p[1]->mapQ;
if (p[0]->mapQ > mapQ_p) p[0]->mapQ = mapQ_p;
} else { // both ends moved
p[0]->seQ = p[1]->seQ = 0;
......
......@@ -87,7 +87,7 @@ static void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt[2], int n_seqs, bwa_seq
if (seqs[i].len > max_len) max_len = seqs[i].len;
if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
stack = gap_init_stack(opt->max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
seed_w[0] = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
seed_w[1] = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
......
......@@ -169,6 +169,7 @@ void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac)
new_nt_read = cs2nt_nt_qual(len, nt_read, cs_read, tarray);
// update p
--p->full_len;
p->len = len - 1;
for (i = 0; i < p->len; ++i) {
if ((new_nt_read[i]&0x3f) == 63) {
......
......@@ -3,7 +3,7 @@
#include "main.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.5.4 (r1245)"
#define PACKAGE_VERSION "0.5.5 (r1273)"
#endif
static int usage()
......
#!/usr/bin/perl -w
use strict;
use warnings;
die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);
my ($fhs, $fhq, $q);
open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
$/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
while (<$fhs>) {
$q = <$fhq>;
print "\@$_";
$/ = ">";
$_ = <$fhs>; $q = <$fhq>;
chomp; chomp($q);
$q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
print $_, "+\n";
for (my $i = 0; $i < length($q); $i += 60) {
print substr($q, $i, 60), "\n";
}
$/ = "\n";
}
close($fhs); close($fhq);
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