xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-07 06:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

avoid misassemblies; better polyploidy graph

Browse Source
This commit is contained in:
chhylp123
2023-03-22 12:23:53 -04:00
parent d4773a497f
commit 86b7dd424a
12 changed files with 1931 additions and 79 deletions
Download Patch File Download Diff File Expand all files Collapse all files
anchor.cpp
+16 -2
View File
@@ -1620,7 +1620,7 @@ inline uint64_t special_lchain(Candidates_list* cl, overlap_region_alloc* ol, ui
double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off, double mcopy_rate, uint32_t mcopy_khit_cut,
st_mt_t *sp, uint64_t *si, uint64_t m, uint64_t l, uint64_t k)
{
uint64_t z, s, e, yid, ol0 = ol->length, ol1;
uint64_t z, s, e, yid, ol0 = ol->length, ol1, m0 = m;
if(l >= k) return m;
yid = cl->list[l].readID;
for (z = l; z < k && cl->list[z].strand == cl->list[l].strand; z++);
@@ -1678,7 +1678,21 @@ inline uint64_t special_lchain(Candidates_list* cl, overlap_region_alloc* ol, ui
}
s++;
}
ol->length = s;
if(s != ol->length) {
ol->length = s;
for (z = ol0; z < ol->length; z++) {
s = ol->list[z].non_homopolymer_errors;
pi = cl->list[s].readID;
ol->list[z].non_homopolymer_errors = m0;
for (; s < m && cl->list[s].readID == pi; s++) {
cl->list[m0] = cl->list[s];
cl->list[m0].readID = z; m0++;
}
}
m = m0;
}
}
return m;
}