Commit 9b4cfaa2 authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 0.7.15

parent 11ce18b5
Release 0.7.15 (31 May 2016)
----------------------------
Fixed a long existing bug which potentially leads underestimated insert size
upper bound. This bug should have little effect in practice.
(0.7.15: 31 May 2016, r1140)
Release 0.7.14 (4 May 2016)
---------------------------
In the ALT mapping mode, this release adds the "AH:*" header tag to SQ lines
corresponding to alternate haplotypes.
(0.7.14: 4 May 2016, r1136)
Release 0.7.13 (23 Feburary 2016)
---------------------------------
......
.TH bwa 1 "23 December 2014" "bwa-0.7.12-r1034" "Bioinformatics tools"
.TH bwa 1 "31 May 2016" "bwa-0.7.15-r1140" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
......@@ -202,7 +202,7 @@ Discard a MEM if it has more than
.I INT
occurence in the genome. This is an insensitive parameter. [500]
.TP
.BI -D \ INT
.BI -D \ FLOAT
Drop chains shorter than
.I FLOAT
fraction of the longest overlapping chain [0.5]
......
......@@ -379,8 +379,11 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
}
}
if (n_SQ == 0) {
for (i = 0; i < bns->n_seqs; ++i)
err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
for (i = 0; i < bns->n_seqs; ++i) {
err_printf("@SQ\tSN:%s\tLN:%d", bns->anns[i].name, bns->anns[i].len);
if (bns->anns[i].is_alt) err_printf("\tAH:*\n");
else err_fputc('\n', stdout);
}
} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
if (hdr_line) err_printf("%s\n", hdr_line);
......
......@@ -5,7 +5,7 @@ use warnings;
use Getopt::Std;
my %opts = (t=>1);
getopts("SadskHo:R:x:t:", \%opts);
getopts("PSadskHo:R:x:t:", \%opts);
die('
Usage: run-bwamem [options] <idxbase> <file1> [file2]
......@@ -151,7 +151,7 @@ $cmd .= " | $root/bwa mem $bwa_opts$ARGV[0] - 2> $prefix.log.bwamem \\\n";
$cmd .= " | $root/samblaster 2> $prefix.log.dedup \\\n" if defined($opts{d});
my $has_hla = 0;
if (-f "$ARGV[0].alt") {
if (-f "$ARGV[0].alt" && !defined($opts{P})) {
my $fh;
open($fh, "$ARGV[0].alt") || die;
while (<$fh>) {
......
......@@ -94,7 +94,7 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
r->low = (int)(p25 - MAPPING_BOUND * (p75 - p25) + .499);
r->high = (int)(p75 + MAPPING_BOUND * (p75 - p25) + .499);
if (r->low > r->avg - MAX_STDDEV * r->std) r->low = (int)(r->avg - MAX_STDDEV * r->std + .499);
if (r->high < r->avg - MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
if (r->high < r->avg + MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
if (r->low < 1) r->low = 1;
fprintf(stderr, "[M::%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r->low, r->high);
free(q->a);
......
......@@ -82,7 +82,7 @@ bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
r.high = (int)(p75 + 3. * (p75 - p25) + .499);
if (r.low > r.avg - MAX_STDDEV * r.std) r.low = (int)(r.avg - MAX_STDDEV * r.std + .499);
r.low = tmp > max_len? tmp : max_len;
if (r.high < r.avg - MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
if (r.high < r.avg + MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
free(isize);
return r;
......
......@@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.13-r1126"
#define PACKAGE_VERSION "0.7.15-r1140"
#endif
int bwa_fa2pac(int argc, char *argv[]);
......
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