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print msg to stderr; output more in fastmap

This commit is contained in:
Heng Li 2011-10-25 15:06:13 -04:00
parent 7664795ffb
commit 55059443bd
2 changed files with 32 additions and 9 deletions
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4
bwt_gen.c
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@ -1486,8 +1486,8 @@ BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxB
BWTIncConstruct(bwtInc, textToLoad); BWTIncConstruct(bwtInc, textToLoad);
processedTextLength += textToLoad; processedTextLength += textToLoad;
if (bwtInc->numberOfIterationDone % 10 == 0) { if (bwtInc->numberOfIterationDone % 10 == 0) {
printf("[BWTIncConstructFromPacked] %lu iterations done. %lu characters processed.\n", fprintf(stderr, "[BWTIncConstructFromPacked] %lu iterations done. %lu characters processed.\n",
(long)bwtInc->numberOfIterationDone, (long)processedTextLength); (long)bwtInc->numberOfIterationDone, (long)processedTextLength);
} }
} }
return bwtInc; return bwtInc;

37
fastmap.c
View File

@ -1,6 +1,8 @@
#include <zlib.h> #include <zlib.h>
#include <unistd.h>
#include <stdio.h> #include <stdio.h>
#include <unistd.h>
#include <stdlib.h>
#include "bntseq.h"
#include "bwt.h" #include "bwt.h"
#include "kvec.h" #include "kvec.h"
#include "kseq.h" #include "kseq.h"
@ -10,28 +12,37 @@ extern unsigned char nst_nt4_table[256];
int main_fastmap(int argc, char *argv[]) int main_fastmap(int argc, char *argv[])
{ {
int c, i; int c, i, min_iwidth = 3, min_len = 17;
kseq_t *seq; kseq_t *seq;
bwtint_t k;
gzFile fp; gzFile fp;
bwt_t *bwt; bwt_t *bwt;
bntseq_t *bns;
bwtintv_v a[3], mem, *tvec[3]; bwtintv_v a[3], mem, *tvec[3];
while ((c = getopt(argc, argv, "")) >= 0) {
while ((c = getopt(argc, argv, "w:l:")) >= 0) {
switch (c) { switch (c) {
case 'w': min_iwidth = atoi(optarg); break;
case 'l': min_len = atoi(optarg); break;
} }
} }
if (optind + 1 >= argc) { if (optind + 1 >= argc) {
fprintf(stderr, "bwa fastmap <idxbase> <in.fq>\n"); fprintf(stderr, "bwa fastmap <idxbase> <in.fq>\n");
return 1; return 1;
} }
fp = gzopen(argv[optind + 1], "r"); fp = gzopen(argv[optind + 1], "r");
seq = kseq_init(fp); seq = kseq_init(fp);
{ // load the BWT { // load the packed sequences, BWT and SA
char *tmp = calloc(strlen(argv[optind]) + 5, 1); char *tmp = calloc(strlen(argv[optind]) + 5, 1);
strcat(strcpy(tmp, argv[optind]), ".bwt"); strcat(strcpy(tmp, argv[optind]), ".bwt");
bwt = bwt_restore_bwt(tmp); bwt = bwt_restore_bwt(tmp);
strcat(strcpy(tmp, argv[optind]), ".sa");
bwt_restore_sa(tmp, bwt);
free(tmp); free(tmp);
bns = bns_restore(argv[optind]);
} }
for (i = 0; i < 3; ++i) { for (i = 0; i < 3; ++i) { // initiate the temporary array
kv_init(a[i]); kv_init(a[i]);
tvec[i] = &a[i]; tvec[i] = &a[i];
} }
@ -40,15 +51,27 @@ int main_fastmap(int argc, char *argv[])
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]];
bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec); bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec);
printf(">%s\t%ld\n", seq->name.s, mem.n); printf(">%s\t%ld\n", seq->name.s, seq->seq.l);
for (i = 0; i < mem.n; ++i) { for (i = 0; i < mem.n; ++i) {
bwtintv_t *p = &mem.a[i]; bwtintv_t *p = &mem.a[i];
printf("%d\t%d\t%ld\n", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]); if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
printf("%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
if (p->x[2] <= min_iwidth) {
for (k = 0; k < p->x[2]; ++k) {
int is_rev;
int64_t pos;
pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev);
printf("\t%c%ld", is_rev?'-':'+', (long)pos);
}
}
putchar('\n');
} }
puts("//"); puts("//");
} }
free(mem.a); free(mem.a);
for (i = 0; i < 3; ++i) free(a[i].a); for (i = 0; i < 3; ++i) free(a[i].a);
bns_destroy(bns);
bwt_destroy(bwt); bwt_destroy(bwt);
kseq_destroy(seq); kseq_destroy(seq);
gzclose(fp); gzclose(fp);