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r708: implemented double Z-drop thresholds (#112)

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When aligning long reads, we would prefer to align through low-quality
regions. This requires a large Z-drop threshold. However, to find small
inversions, we need to use a small Z-drop. This commit address this
conflict with two Z-drop thresholds. When Z-drop exceeds the smaller
threshold, we perform a local alignment to check if there is a potential
inversion. If there is one, we break the alignment; otherwise we break
the alignment only if Z-drop excess the larger threshold.

This commit also fixes a bug that reported wrong coordinates when the
inversion is on the forward strand (#112).
This commit is contained in:
Heng Li
2018-02-15 10:50:49 -05:00
parent c0e0d5d84b
commit 1372977a37
6 changed files with 77 additions and 39 deletions
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minimap.h
+2 -2
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@@ -82,7 +82,7 @@ typedef struct {
int32_t mlen, blen; // seeded exact match length; seeded alignment block length
int32_t n_sub; // number of suboptimal mappings
int32_t score0; // initial chaining score (before chain merging/spliting)
uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, seg_id:8, dummy:8;
uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, seg_id:8, split_inv:1, dummy:7;
uint32_t hash;
float div;
mm_extra_t *p;
@@ -116,7 +116,7 @@ typedef struct {
int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
int noncan; // cost of non-canonical splicing sites
int zdrop; // break alignment if alignment score drops too fast along the diagonal
int zdrop, zdrop_inv; // break alignment if alignment score drops too fast along the diagonal
int end_bonus;
int min_dp_max; // drop an alignment if the score of the max scoring segment is below this threshold
int min_ksw_len;