57 lines
1.3 KiB
C
57 lines
1.3 KiB
C
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#include <zlib.h>
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#include <unistd.h>
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#include <stdio.h>
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#include "bwt.h"
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#include "kvec.h"
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#include "kseq.h"
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KSEQ_INIT(gzFile, gzread)
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extern unsigned char nst_nt4_table[256];
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int main_fastmap(int argc, char *argv[])
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{
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int c, i;
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kseq_t *seq;
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gzFile fp;
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bwt_t *bwt;
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bwtintv_v a[3], mem, *tvec[3];
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while ((c = getopt(argc, argv, "")) >= 0) {
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switch (c) {
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}
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}
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if (optind + 1 >= argc) {
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fprintf(stderr, "bwa fastmap <idxbase> <in.fq>\n");
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return 1;
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}
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fp = gzopen(argv[optind + 1], "r");
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seq = kseq_init(fp);
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{ // load the BWT
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char *tmp = calloc(strlen(argv[optind]) + 5, 1);
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strcat(strcpy(tmp, argv[optind]), ".bwt");
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bwt = bwt_restore_bwt(tmp);
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free(tmp);
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}
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for (i = 0; i < 3; ++i) {
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kv_init(a[i]);
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tvec[i] = &a[i];
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}
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kv_init(mem);
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while (kseq_read(seq) >= 0) {
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for (i = 0; i < seq->seq.l; ++i)
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seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
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bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec);
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printf(">%s\t%ld\n", seq->name.s, mem.n);
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for (i = 0; i < mem.n; ++i) {
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bwtintv_t *p = &mem.a[i];
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printf("%d\t%d\t%ld\n", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
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}
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puts("//");
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}
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free(mem.a);
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for (i = 0; i < 3; ++i) free(a[i].a);
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bwt_destroy(bwt);
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kseq_destroy(seq);
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gzclose(fp);
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return 0;
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}
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