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r188: renamed bseq* to mm_bseq*

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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
This commit is contained in:
Heng Li
2017-07-19 09:26:46 -04:00
parent b9b0b6f49c
commit 71c988f6ab
10 changed files with 65 additions and 57 deletions
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bseq.c
+10 -10
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@@ -7,43 +7,43 @@
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
struct bseq_file_s {
struct mm_bseq_file_s {
int is_eof;
gzFile fp;
kseq_t *ks;
};
bseq_file_t *bseq_open(const char *fn)
mm_bseq_file_t *mm_bseq_open(const char *fn)
{
bseq_file_t *fp;
mm_bseq_file_t *fp;
gzFile f;
f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (f == 0) return 0;
fp = (bseq_file_t*)calloc(1, sizeof(bseq_file_t));
fp = (mm_bseq_file_t*)calloc(1, sizeof(mm_bseq_file_t));
fp->fp = f;
fp->ks = kseq_init(fp->fp);
return fp;
}
void bseq_close(bseq_file_t *fp)
void mm_bseq_close(mm_bseq_file_t *fp)
{
kseq_destroy(fp->ks);
gzclose(fp->fp);
free(fp);
}
bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
{
int size = 0, m, n;
bseq1_t *seqs;
mm_bseq1_t *seqs;
kseq_t *ks = fp->ks;
m = n = 0; seqs = 0;
while (kseq_read(ks) >= 0) {
bseq1_t *s;
mm_bseq1_t *s;
assert(ks->seq.l <= INT32_MAX);
if (n >= m) {
m = m? m<<1 : 256;
seqs = (bseq1_t*)realloc(seqs, m * sizeof(bseq1_t));
seqs = (mm_bseq1_t*)realloc(seqs, m * sizeof(mm_bseq1_t));
}
s = &seqs[n];
s->name = strdup(ks->name.s);
@@ -58,7 +58,7 @@ bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
return seqs;
}
int bseq_eof(bseq_file_t *fp)
int mm_bseq_eof(mm_bseq_file_t *fp)
{
return fp->is_eof;
}