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better parameters for short reads

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It turns out the key problem is not the minimizer density. It is the max
occurrence that tends to affect results more, especially sensitivity. There is
still lots of work to do, but for now, it seems a good start.
This commit is contained in:
Heng Li
2017-09-12 16:11:23 -04:00
parent eea9e851d8
commit d7f2ac1d4f
3 changed files with 13 additions and 6 deletions
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align.c
+4
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@@ -143,6 +143,10 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
fputc('\n', stderr);
}
if (opt->flag & MM_F_SR) {
flag |= KSW_EZ_APPROX_MAX;
if (flag & KSW_EZ_EXTZ_ONLY) flag |= KSW_EZ_APPROX_DROP;
}
if (opt->flag & MM_F_SPLICE)
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, opt->zdrop, flag, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)