96 lines
2.2 KiB
C
96 lines
2.2 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 "kvec.h"
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#include "kseq.h"
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KSEQ_INIT2(, gzFile, gzread)
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#define CHECK_PAIR_THRES 1000000
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struct mm_bseq_file_s {
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gzFile fp;
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kseq_t *ks;
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mm_bseq1_t s;
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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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static inline int mm_qname_same(const char *s1, const char *s2)
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{
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int l1, l2;
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l1 = strlen(s1);
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l2 = strlen(s2);
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if (l1 != l2 || l1 < 3) return 0;
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if (!(s1[l1-1] >= '1' && s1[l1-1] <= '2' && s1[l1-2] == '/')) return 0;
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if (!(s2[l2-1] >= '1' && s2[l2-1] <= '2' && s2[l2-2] == '/')) return 0;
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return (strncmp(s1, s2, l1 - 2) == 0);
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}
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static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual)
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{
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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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}
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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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int64_t size = 0;
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kvec_t(mm_bseq1_t) a = {0,0,0};
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kseq_t *ks = fp->ks;
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if (fp->s.seq) {
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kv_resize(mm_bseq1_t, 0, a, 256);
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kv_push(mm_bseq1_t, 0, a, fp->s);
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size = fp->s.l_seq;
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memset(&fp->s, 0, sizeof(mm_bseq1_t));
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}
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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 (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
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kv_pushp(mm_bseq1_t, 0, a, &s);
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kseq2bseq(ks, s, with_qual);
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size += s->l_seq;
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if (size >= chunk_size) {
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if (a.a[a.n-1].l_seq < CHECK_PAIR_THRES) {
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while (kseq_read(ks) >= 0) {
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kseq2bseq(ks, &fp->s, with_qual);
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if (mm_qname_same(fp->s.name, a.a[a.n-1].name)) {
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kv_push(mm_bseq1_t, 0, a, fp->s);
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memset(&fp->s, 0, sizeof(mm_bseq1_t));
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} else break;
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}
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}
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break;
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}
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}
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*n_ = a.n;
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return a.a;
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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 (ks_eof(fp->ks->f) && fp->s.seq == 0);
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}
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