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r933: with bwa-postalt ready, drop option -g

This commit is contained in:
Heng Li 2014-10-21 00:23:14 -04:00
parent 2bfa3c767b
commit 76a15ea91b
4 changed files with 3 additions and 9 deletions
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5
bwamem.c
View File

@ -79,7 +79,6 @@ mem_opt_t *mem_opt_init()
o->min_chain_weight = 0;
o->max_chain_extend = 1<<30;
o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len);
o->min_pa_ratio = 0;
bwa_fill_scmat(o->a, o->b, o->mat);
return o;
}
@ -841,7 +840,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
if (p->rid >= 0) { // with coordinate
kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME
kputl(p->pos + 1, str); kputc('\t', str); // POS
kputw(p->score < opt->min_pa_ratio * p->alt_sc? 0 : p->mapq, str); kputc('\t', str); // MAPQ
kputw(p->mapq, str); kputc('\t', str); // MAPQ
if (p->n_cigar) { // aligned
for (i = 0; i < p->n_cigar; ++i) {
int c = p->cigar[i]&0xf;
@ -931,8 +930,6 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
}
if (p->alt_sc > 0)
ksprintf(str, "\tpa:f:%.3f", (double)p->score / p->alt_sc);
if (p->score < opt->min_pa_ratio * p->alt_sc)
ksprintf(str, "\tom:i:%d", p->mapq);
}
if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
if (s->comment) { kputc('\t', str); kputs(s->comment, str); }

1
bwamem.h
View File

@ -48,7 +48,6 @@ typedef struct {
float XA_drop_ratio; // when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
float mask_level_redun;
float mapQ_coef_len;
float min_pa_ratio;
int mapQ_coef_fac;
int max_ins; // when estimating insert size distribution, skip pairs with insert longer than this value
int max_matesw; // perform maximally max_matesw rounds of mate-SW for each end

4
fastmap.c
View File

@ -55,7 +55,7 @@ int main_mem(int argc, char *argv[])
opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:g:")) >= 0) {
while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@ -85,7 +85,6 @@ int main_mem(int argc, char *argv[])
else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
else if (c == 'g') opt->min_pa_ratio = atof(optarg), opt0.min_pa_ratio = 1;
else if (c == 'C') copy_comment = 1;
else if (c == 'K') fixed_chunk_size = atoi(optarg);
else if (c == 'h') {
@ -172,7 +171,6 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -j ignore ALT contigs\n");
fprintf(stderr, "\n");
fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
fprintf(stderr, " -g FLOAT set mapQ to zero if the ratio of the primary-to-alt scores below FLOAT [%.3f]\n", opt->min_pa_ratio);
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -h INT[,INT] if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r930-dirty"
#define PACKAGE_VERSION "0.7.10-r933-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);