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r466: detect multi-part index more smartly

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though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
This commit is contained in:
Heng Li
2017-10-04 17:32:58 -04:00
parent 1554149158
commit 7d50e646dd
7 changed files with 40 additions and 39 deletions
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index.c
+14 -7
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@@ -427,28 +427,28 @@ mm_idx_t *mm_idx_load(FILE *fp)
return mi;
}
int mm_idx_is_idx(const char *fn)
int64_t mm_idx_is_idx(const char *fn)
{
int fd, is_idx = 0;
off_t ret;
off_t ret, off_end;
char magic[4];
if (strcmp(fn, "-") == 0) return 0; // read from pipe; not an index
fd = open(fn, O_RDONLY);
if (fd < 0) return -1; // error
if ((ret = lseek(fd, 0, SEEK_END)) >= 4) {
if ((off_end = lseek(fd, 0, SEEK_END)) >= 4) {
lseek(fd, 0, SEEK_SET);
ret = read(fd, magic, 4);
if (ret == 4 && strncmp(magic, MM_IDX_MAGIC, 4) == 0)
is_idx = 1;
}
close(fd);
return is_idx;
return is_idx? off_end : 0;
}
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out)
{
int is_idx;
int64_t is_idx;
mm_idx_reader_t *r;
is_idx = mm_idx_is_idx(fn);
if (is_idx < 0) return 0; // failed to open the index
@@ -456,8 +456,10 @@ mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, cons
r->is_idx = is_idx;
if (opt) r->opt = *opt;
else mm_idxopt_init(&r->opt);
if (r->is_idx) r->fp.idx = fopen(fn, "rb");
else r->fp.seq = mm_bseq_open(fn);
if (r->is_idx) {
r->fp.idx = fopen(fn, "rb");
r->idx_size = is_idx;
} else r->fp.seq = mm_bseq_open(fn);
if (fn_out) r->fp_out = fopen(fn_out, "wb");
return r;
}
@@ -485,3 +487,8 @@ mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
}
return mi;
}
int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases, mm_bseq_eof() might not work
{
return r->is_idx? (feof(r->fp.idx) || ftell(r->fp.idx) == r->idx_size) : mm_bseq_eof(r->fp.seq);
}