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dev-r452: allow to specify insert size at cmd 

This is also very useful for debugging.
This commit is contained in:
Heng Li 2014-03-31 11:21:03 -04:00
parent 417c6d66c7
commit b7076d9023
2 changed files with 28 additions and 5 deletions
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31
fastmap.c
View File

@ -2,6 +2,7 @@
#include <stdio.h>
#include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include "bwa.h"
@ -28,9 +29,13 @@ int main_mem(int argc, char *argv[])
char *p, *rg_line = 0;
void *ko = 0, *ko2 = 0;
int64_t n_processed = 0;
mem_pestat_t pes[4], *pes0 = 0;
memset(pes, 0, 4 * sizeof(mem_pestat_t));
for (i = 0; i < 4; ++i) pes[i].failed = 1;
opt = mem_opt_init();
while ((c = getopt(argc, argv, "epaMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:")) >= 0) {
while ((c = getopt(argc, argv, "epaMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg);
else if (c == 'w') opt->w = atoi(optarg);
else if (c == 'A') opt->a = atoi(optarg);
@ -50,6 +55,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'r') opt->split_factor = atof(optarg);
else if (c == 'D') opt->chain_drop_ratio = atof(optarg);
else if (c == 'm') opt->max_matesw = atoi(optarg);
else if (c == 's') opt->split_width = atoi(optarg);
else if (c == 'C') copy_comment = 1;
else if (c == 'Q') {
opt->mapQ_coef_len = atoi(optarg);
@ -68,7 +74,21 @@ int main_mem(int argc, char *argv[])
opt->pen_clip3 = strtol(p+1, &p, 10);
} else if (c == 'R') {
if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
} else if (c == 's') opt->split_width = atoi(optarg);
} else if (c == 'I') { // specify the insert size distribution
pes0 = pes;
pes[1].failed = 0;
pes[1].avg = strtod(optarg, &p);
pes[1].std = pes[1].avg * .1;
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
pes[1].std = strtod(p+1, &p);
pes[1].high = (int)(pes[1].avg + 4. * pes[1].std + .499);
pes[1].low = (int)(pes[1].avg - 4. * pes[1].std + .499);
if (pes[1].low < 1) pes[1].low = 1;
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
pes[1].high = (int)(strtod(p+1, &p) + .499);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
pes[1].low = (int)(strtod(p+1, &p) + .499);
}
else return 1;
}
if (opt->n_threads < 1) opt->n_threads = 1;
@ -102,7 +122,10 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
fprintf(stderr, " -M mark shorter split hits as secondary (for Picard/GATK compatibility)\n");
fprintf(stderr, " -M mark shorter split hits as secondary\n\n");
fprintf(stderr, " -I FLOAT[,FLOAT[,INT[,INT]]]\n");
fprintf(stderr, " specify the mean, standard deviation (10%% of mean), max (4 sigma from the mean)\n");
fprintf(stderr, " and min of the insert size distribution. FR orientation only. [inferred]\n");
fprintf(stderr, "\nNote: Please read the man page for detailed description of the command line and options.\n");
fprintf(stderr, "\n");
free(opt);
@ -149,7 +172,7 @@ int main_mem(int argc, char *argv[])
for (i = 0; i < n; ++i) size += seqs[i].l_seq;
if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, n, (long)size);
mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n_processed, n, seqs, 0);
mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n_processed, n, seqs, pes0);
n_processed += n;
for (i = 0; i < n; ++i) {
err_fputs(seqs[i].sam, stdout);

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.7+dev-r451"
#define PACKAGE_VERSION "0.7.7+dev-r452"
#endif
int bwa_fa2pac(int argc, char *argv[]);