65 lines
1.3 KiB
C
65 lines
1.3 KiB
C
#include <zlib.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <assert.h>
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#include "bseq.h"
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#include "kseq.h"
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KSEQ_INIT(gzFile, gzread)
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struct mm_bseq_file_s {
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int is_eof;
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gzFile fp;
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kseq_t *ks;
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};
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mm_bseq_file_t *mm_bseq_open(const char *fn)
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{
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mm_bseq_file_t *fp;
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gzFile f;
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f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
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if (f == 0) return 0;
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fp = (mm_bseq_file_t*)calloc(1, sizeof(mm_bseq_file_t));
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fp->fp = f;
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fp->ks = kseq_init(fp->fp);
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return fp;
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}
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void mm_bseq_close(mm_bseq_file_t *fp)
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{
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kseq_destroy(fp->ks);
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gzclose(fp->fp);
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free(fp);
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}
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mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
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{
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int size = 0, m, n;
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mm_bseq1_t *seqs;
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kseq_t *ks = fp->ks;
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m = n = 0; seqs = 0;
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while (kseq_read(ks) >= 0) {
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mm_bseq1_t *s;
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assert(ks->seq.l <= INT32_MAX);
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if (n >= m) {
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m = m? m<<1 : 256;
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seqs = (mm_bseq1_t*)realloc(seqs, m * sizeof(mm_bseq1_t));
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}
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s = &seqs[n];
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s->name = strdup(ks->name.s);
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s->seq = strdup(ks->seq.s);
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s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;
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s->l_seq = ks->seq.l;
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size += seqs[n++].l_seq;
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if (size >= chunk_size) break;
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}
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if (size < chunk_size) fp->is_eof = 1;
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*n_ = n;
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return seqs;
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}
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int mm_bseq_eof(mm_bseq_file_t *fp)
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{
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return fp->is_eof;
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}
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