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r876: optionally ignore idxbase.alt file

This commit is contained in:
Heng Li 2014-09-27 23:21:50 -04:00
parent dae4ca3ced
commit 0a2cf98293
2 changed files with 9 additions and 4 deletions
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11
fastmap.c
View File

@ -10,8 +10,8 @@
#include "bwamem.h" #include "bwamem.h"
#include "kvec.h" #include "kvec.h"
#include "utils.h" #include "utils.h"
#include "bntseq.h"
#include "kseq.h" #include "kseq.h"
#include "utils.h"
KSEQ_DECLARE(gzFile) KSEQ_DECLARE(gzFile)
extern unsigned char nst_nt4_table[256]; extern unsigned char nst_nt4_table[256];
@ -38,7 +38,7 @@ static void update_a(mem_opt_t *opt, const mem_opt_t *opt0)
int main_mem(int argc, char *argv[]) int main_mem(int argc, char *argv[])
{ {
mem_opt_t *opt, opt0; mem_opt_t *opt, opt0;
int fd, fd2, i, c, n, copy_comment = 0; int fd, fd2, i, c, n, copy_comment = 0, ignore_alt = 0;
int fixed_chunk_size = -1, actual_chunk_size; int fixed_chunk_size = -1, actual_chunk_size;
gzFile fp, fp2 = 0; gzFile fp, fp2 = 0;
kseq_t *ks, *ks2 = 0; kseq_t *ks, *ks2 = 0;
@ -55,7 +55,7 @@ int main_mem(int argc, char *argv[])
opt = mem_opt_init(); opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t)); memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "epaFMCSPHVYk: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:g:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1; if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'x') mode = optarg; else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1; else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@ -76,6 +76,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1; 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 == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
else if (c == 'v') bwa_verbose = atoi(optarg); else if (c == 'v') bwa_verbose = atoi(optarg);
else if (c == 'j') ignore_alt = 1;
else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.; else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.;
else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.; else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.;
else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1; else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1;
@ -168,6 +169,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, "\nInput/output options:\n\n"); fprintf(stderr, "\nInput/output options:\n\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n"); fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n"); fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
fprintf(stderr, " -j ignore ALT contigs\n");
fprintf(stderr, "\n"); fprintf(stderr, "\n");
fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose); 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, " -g FLOAT set mapQ to zero if the ratio of the primary-to-alt scores below FLOAT [%.3f]\n", opt->min_pa_ratio);
@ -229,6 +231,9 @@ int main_mem(int argc, char *argv[])
bwa_fill_scmat(opt->a, opt->b, opt->mat); bwa_fill_scmat(opt->a, opt->b, opt->mat);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
if (ignore_alt)
for (i = 0; i < idx->bns->n_seqs; ++i)
idx->bns->anns[i].is_alt = 0;
ko = kopen(argv[optind + 1], &fd); ko = kopen(argv[optind + 1], &fd);
if (ko == 0) { if (ko == 0) {

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r875-dirty" #define PACKAGE_VERSION "0.7.10-r876-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);