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separate out spliced alignment; not right yet

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Heng Li
2017-08-12 18:54:32 -04:00
parent 53b3265d84
commit 61eef0575c
5 changed files with 332 additions and 28 deletions
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align.c
+1 -1
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@@ -136,7 +136,7 @@ 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_SPLICE)
ksw_extd2_noins_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, 0, -1, opt->zdrop, flag, ez);
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->zdrop, flag, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, opt->zdrop, flag, ez);
else