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fastmap: optionally output the original query seq

This commit is contained in:
Heng Li 2011-11-24 19:44:21 -05:00
parent 150bfbdef4
commit bf65b6463a
2 changed files with 10 additions and 5 deletions
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13
fastmap.c
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@ -55,7 +55,7 @@ int smem_next(smem_i *iter)
int main_fastmap(int argc, char *argv[]) int main_fastmap(int argc, char *argv[])
{ {
int c, i, min_iwidth = 20, min_len = 17; int c, i, min_iwidth = 20, min_len = 17, print_seq = 0;
kseq_t *seq; kseq_t *seq;
bwtint_t k; bwtint_t k;
gzFile fp; gzFile fp;
@ -63,14 +63,15 @@ int main_fastmap(int argc, char *argv[])
bntseq_t *bns; bntseq_t *bns;
smem_i *iter; smem_i *iter;
while ((c = getopt(argc, argv, "w:l:")) >= 0) { while ((c = getopt(argc, argv, "w:l:s")) >= 0) {
switch (c) { switch (c) {
case 's': print_seq = 1; break;
case 'w': min_iwidth = atoi(optarg); break; case 'w': min_iwidth = atoi(optarg); break;
case 'l': min_len = atoi(optarg); break; case 'l': min_len = atoi(optarg); break;
} }
} }
if (optind + 1 >= argc) { if (optind + 1 >= argc) {
fprintf(stderr, "Usage: bwa fastmap [-l minLen=%d] [-w maxSaSize=%d] <idxbase> <in.fq>\n", min_len, min_iwidth); fprintf(stderr, "Usage: bwa fastmap [-s] [-l minLen=%d] [-w maxSaSize=%d] <idxbase> <in.fq>\n", min_len, min_iwidth);
return 1; return 1;
} }
@ -87,9 +88,13 @@ int main_fastmap(int argc, char *argv[])
} }
iter = smem_iter_init(bwt); iter = smem_iter_init(bwt);
while (kseq_read(seq) >= 0) { while (kseq_read(seq) >= 0) {
printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
if (print_seq) {
putchar('\t');
puts(seq->seq.s);
} else putchar('\n');
for (i = 0; i < seq->seq.l; ++i) for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]]; seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
printf("SQ\t%s\t%ld\n", seq->name.s, seq->seq.l);
smem_set_query(iter, seq->seq.l, (uint8_t*)seq->seq.s); smem_set_query(iter, seq->seq.l, (uint8_t*)seq->seq.s);
while (smem_next(iter) > 0) { while (smem_next(iter) > 0) {
for (i = 0; i < iter->matches->n; ++i) { for (i = 0; i < iter->matches->n; ++i) {

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.6.0-r100-dev" #define PACKAGE_VERSION "0.6.0-r102-dev"
#endif #endif
static int usage() static int usage()