134 lines
3.9 KiB
C
134 lines
3.9 KiB
C
#include <zlib.h>
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#include <stdio.h>
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#include <stdlib.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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unsigned char seq_comp_table[256] = {
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0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
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16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
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32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
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48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
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64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
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'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
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64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
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'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,
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128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
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144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
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160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
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176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
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192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
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208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
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224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
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240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255
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};
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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 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_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int frag_mode, 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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*n_ = 0;
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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 (frag_mode && 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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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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return mm_bseq_read2(fp, chunk_size, with_qual, 0, n_);
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}
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mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int *n_)
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{
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int i;
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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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*n_ = 0;
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if (n_fp < 1) return 0;
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while (1) {
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for (i = 0; i < n_fp; ++i)
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if (kseq_read(fp[i]->ks) < 0)
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break;
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if (i != n_fp) break; // some file reaches the end
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if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
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for (i = 0; i < n_fp; ++i) {
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mm_bseq1_t *s;
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kv_pushp(mm_bseq1_t, 0, a, &s);
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kseq2bseq(fp[i]->ks, s, with_qual);
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size += s->l_seq;
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}
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if (size >= chunk_size) break;
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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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