fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-01 00:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r466: detect multi-part index more smartly

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files
format.c
+7 -9
View File
@@ -105,10 +105,15 @@ err_set_rg:
free(rg_line);
}
void mm_write_sam_hdr_no_SQ(const char *rg, const char *ver, int argc, char *argv[])
void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
{
kstring_t str = {0,0,0};
sam_write_rg_line(&str, rg);
if (idx) {
uint32_t i;
for (i = 0; i < idx->n_seq; ++i)
printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
}
if (rg) sam_write_rg_line(&str, rg);
mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
if (ver) mm_sprintf_lite(&str, "\tVN:%s", ver);
if (argc > 1) {
@@ -213,13 +218,6 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
write_cs(km, s, mi, t, r);
}
void mm_write_sam_SQ(const mm_idx_t *idx)
{
uint32_t i;
for (i = 0; i < idx->n_seq; ++i)
printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
}
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
{
extern unsigned char seq_comp_table[256];