Commit 592e634b authored by Andreas Tille's avatar Andreas Tille

New upstream version 0.7.17

parent 6b5aa132
Release 0.7.17 (23 October 2017)
--------------------------------
This release adds option -q to preserve the mapping quality of split alignment
with a lower alignment score than the primary alignment. Option -5
automatically applies -q as well.
(0.7.17: 23 October 2017, r1188)
Release 0.7.16 (30 July 2017)
-----------------------------
......
.TH bwa 1 "30 July 2017" "bwa-0.7.16-r1180" "Bioinformatics tools"
.TH bwa 1 "23 October 2017" "bwa-0.7.17-r1188" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
......@@ -303,9 +303,14 @@ For compatibility with other BWA commands, this option may also be given as
.IR FILE .
[standard ouptut]
.TP
.B -q
Don't reduce the mapping quality of split alignment of lower alignment score.
.TP
.B -5
For split alignment, mark the segment with the smallest coordinate as the
primary. This option may help some Hi-C pipelines. By default, BWA-MEM marks
primary. It automatically applies option
.B -q
as well. This option may help some Hi-C pipelines. By default, BWA-MEM marks
highest scoring segment as primary.
.TP
.B -K \ INT
......
......@@ -1026,7 +1026,8 @@ void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
if (l && p->secondary < 0) // if supplementary
q->flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
if (l && !p->is_alt && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
if (!(opt->flag & MEM_F_KEEP_SUPP_MAPQ) && l && !p->is_alt && q->mapq > aa.a[0].mapq)
q->mapq = aa.a[0].mapq; // lower mapq for supplementary mappings, unless -5 or -q is applied
++l;
}
if (aa.n == 0) { // no alignments good enough; then write an unaligned record
......
......@@ -20,6 +20,7 @@ typedef struct __smem_i smem_i;
#define MEM_F_SOFTCLIP 0x200
#define MEM_F_SMARTPE 0x400
#define MEM_F_PRIMARY5 0x800
#define MEM_F_KEEP_SUPP_MAPQ 0x1000
typedef struct {
int a, b; // match score and mismatch penalty
......
......@@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
aux.opt = opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
while ((c = getopt(argc, argv, "51qpaMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == '1') no_mt_io = 1;
else if (c == 'x') mode = optarg;
......@@ -147,7 +147,8 @@ int main_mem(int argc, char *argv[])
else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
else if (c == '5') opt->flag |= MEM_F_PRIMARY5;
else if (c == '5') opt->flag |= MEM_F_PRIMARY5 | MEM_F_KEEP_SUPP_MAPQ; // always apply MEM_F_KEEP_SUPP_MAPQ with -5
else if (c == 'q') opt->flag |= MEM_F_KEEP_SUPP_MAPQ;
else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
else if (c == 'v') bwa_verbose = atoi(optarg);
......@@ -268,7 +269,8 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n");
fprintf(stderr, " -o FILE sam file to output results to [stdout]\n");
fprintf(stderr, " -j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
fprintf(stderr, " -5 for split alignment, take the alignment with the smallest coordiate as primary\n");
fprintf(stderr, " -5 for split alignment, take the alignment with the smallest coordinate as primary\n");
fprintf(stderr, " -q don't modify mapQ of supplementary alignments\n");
fprintf(stderr, " -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) []\n");
fprintf(stderr, "\n");
fprintf(stderr, " -v INT verbosity level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
......
......@@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.16a-r1181"
#define PACKAGE_VERSION "0.7.17-r1188"
#endif
int bwa_fa2pac(int argc, char *argv[]);
......
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