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r477: renamed multi_seg to frag_mode

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This commit is contained in:
Heng Li
2017-10-05 15:48:17 -04:00
parent ae2adf04d4
commit 9c5767f9ed
5 changed files with 25 additions and 24 deletions
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bseq.c
+3 -3
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@@ -61,7 +61,7 @@ static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual)
s->l_seq = ks->seq.l;
}
mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int check_name, int *n_)
mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int frag_mode, int *n_)
{
int64_t size = 0;
kvec_t(mm_bseq1_t) a = {0,0,0};
@@ -81,7 +81,7 @@ mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
kseq2bseq(ks, s, with_qual);
size += s->l_seq;
if (size >= chunk_size) {
if (check_name && a.a[a.n-1].l_seq < CHECK_PAIR_THRES) {
if (frag_mode && a.a[a.n-1].l_seq < CHECK_PAIR_THRES) {
while (kseq_read(ks) >= 0) {
kseq2bseq(ks, &fp->s, with_qual);
if (mm_qname_same(fp->s.name, a.a[a.n-1].name)) {
@@ -102,7 +102,7 @@ mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
return mm_bseq_read2(fp, chunk_size, with_qual, 0, n_);
}
mm_bseq1_t *mm_bseq_read_multi(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int *n_)
mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int *n_)
{
int i;
int64_t size = 0;