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Copy pathbseq.c
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169 lines (156 loc) · 5.24 KB
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#include <zlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#define __STDC_LIMIT_MACROS
#include "bseq.h"
#include "kvec.h"
#include "kseq.h"
KSEQ_INIT2(, gzFile, gzread)
unsigned char seq_comp_table[256] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
96, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,
128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255
};
#define CHECK_PAIR_THRES 1000000
struct mm_bseq_file_s {
gzFile fp;
kseq_t *ks;
mm_bseq1_t s;
};
mm_bseq_file_t *mm_bseq_open(const char *fn)
{
mm_bseq_file_t *fp;
gzFile f;
f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(0, "r");
if (f == 0) return 0;
fp = (mm_bseq_file_t*)calloc(1, sizeof(mm_bseq_file_t));
fp->fp = f;
fp->ks = kseq_init(fp->fp);
return fp;
}
void mm_bseq_close(mm_bseq_file_t *fp)
{
kseq_destroy(fp->ks);
gzclose(fp->fp);
free(fp);
}
static inline char *kstrdup(const kstring_t *s)
{
char *t;
t = (char*)malloc(s->l + 1);
memcpy(t, s->s, s->l + 1);
return t;
}
static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_comment)
{
int i;
if (ks->name.l == 0)
fprintf(stderr, "[WARNING]\033[1;31m empty sequence name in the input.\033[0m\n");
s->name = kstrdup(&ks->name);
s->seq = kstrdup(&ks->seq);
for (i = 0; i < (int)ks->seq.l; ++i) // convert U to T
if (s->seq[i] == 'u' || s->seq[i] == 'U')
--s->seq[i];
s->qual = with_qual && ks->qual.l? kstrdup(&ks->qual) : 0;
s->comment = with_comment && ks->comment.l? kstrdup(&ks->comment) : 0;
s->l_seq = ks->seq.l;
}
mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int with_comment, int frag_mode, int *n_)
{
int64_t size = 0;
int ret;
kvec_t(mm_bseq1_t) a = {0,0,0};
kseq_t *ks = fp->ks;
*n_ = 0;
if (fp->s.seq) {
kv_resize(mm_bseq1_t, 0, a, 256);
kv_push(mm_bseq1_t, 0, a, fp->s);
size = fp->s.l_seq;
memset(&fp->s, 0, sizeof(mm_bseq1_t));
}
while ((ret = kseq_read(ks)) >= 0) {
mm_bseq1_t *s;
assert(ks->seq.l <= INT32_MAX);
if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
kv_pushp(mm_bseq1_t, 0, a, &s);
kseq2bseq(ks, s, with_qual, with_comment);
size += s->l_seq;
if (size >= chunk_size) {
if (frag_mode && a.a[a.n-1].l_seq < CHECK_PAIR_THRES) {
while ((ret = kseq_read(ks)) >= 0) {
kseq2bseq(ks, &fp->s, with_qual, with_comment);
if (mm_qname_same(fp->s.name, a.a[a.n-1].name)) {
kv_push(mm_bseq1_t, 0, a, fp->s);
memset(&fp->s, 0, sizeof(mm_bseq1_t));
} else break;
}
}
break;
}
}
if (ret < -1) {
if (a.n) fprintf(stderr, "[WARNING]\033[1;31m failed to parse the FASTA/FASTQ record next to '%s'. Continue anyway.\033[0m\n", a.a[a.n-1].name);
else fprintf(stderr, "[WARNING]\033[1;31m failed to parse the first FASTA/FASTQ record. Continue anyway.\033[0m\n");
}
*n_ = a.n;
return a.a;
}
mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int frag_mode, int *n_)
{
return mm_bseq_read3(fp, chunk_size, with_qual, 0, frag_mode, n_);
}
mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int *n_)
{
return mm_bseq_read2(fp, chunk_size, with_qual, 0, n_);
}
mm_bseq1_t *mm_bseq_read_frag2(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int with_comment, int *n_)
{
int i;
int64_t size = 0;
kvec_t(mm_bseq1_t) a = {0,0,0};
*n_ = 0;
if (n_fp < 1) return 0;
while (1) {
int n_read = 0;
for (i = 0; i < n_fp; ++i)
if (kseq_read(fp[i]->ks) >= 0)
++n_read;
if (n_read < n_fp) {
if (n_read > 0)
fprintf(stderr, "[W::%s]\033[1;31m query files have different number of records; extra records skipped.\033[0m\n", __func__);
break; // some file reaches the end
}
if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
for (i = 0; i < n_fp; ++i) {
mm_bseq1_t *s;
kv_pushp(mm_bseq1_t, 0, a, &s);
kseq2bseq(fp[i]->ks, s, with_qual, with_comment);
size += s->l_seq;
}
if (size >= chunk_size) break;
}
*n_ = a.n;
return a.a;
}
mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int *n_)
{
return mm_bseq_read_frag2(n_fp, fp, chunk_size, with_qual, 0, n_);
}
int mm_bseq_eof(mm_bseq_file_t *fp)
{
return (ks_eof(fp->ks->f) && fp->s.seq == 0);
}