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r917: added --max-chain-iter to avoid worst case

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Resolves #324
This commit is contained in:
Heng Li
2019-02-27 14:41:01 -05:00
parent ccf1680aaf
commit d431dc0181
8 changed files with 20 additions and 9 deletions
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5
python/cmappy.pxd
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@@ -13,10 +13,11 @@ cdef extern from "minimap.h":
int seed
int sdust_thres
int flag
int max_qlen
int bw
int max_gap, max_gap_ref
int max_frag_len
int max_chain_skip
int max_chain_skip, max_chain_iter
int min_cnt
int min_chain_score
float mask_level
@@ -24,7 +25,7 @@ cdef extern from "minimap.h":
int best_n
int max_join_long, max_join_short
int min_join_flank_sc
float min_join_flank_ratio;
float min_join_flank_ratio
int a, b, q, e, q2, e2
int sc_ambi
int noncan