fb8a1b5536
r542: tuning mapQ calculation
2017-10-31 14:25:09 -04:00
bd04372873
r524: reverted to bwa-mem end bonus
...
and reduced the cost of clipping when filtering by identity
2017-10-20 16:57:31 -04:00
addb61bcb2
r515: more conservative hit exclusion
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When a hit covers a long query subsequence that has not been covered by better
primary hits, this hit is more likely to become a new primary hit.
2017-10-16 13:58:01 -04:00
adf6cd7f52
r513: merged pre- and post-cigar blen and mlen
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This saves a bit memory and is cleaner.
2017-10-16 10:55:18 -04:00
e6f525edaf
r512: option to filter poorly aligned reads
2017-10-16 10:38:22 -04:00
ce06188203
r506: fixed a memory leak
2017-10-12 10:12:22 -04:00
13b66aad4d
r495: fix impropriate CIGAR
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1. Not left aligned
2. In one case, 50M24D50M becomes 24D100M. The leading D needs to be removed.
3. Avoid identical hits after DP
2017-10-10 11:59:44 -04:00
2a1e738a94
r461: randomize repetitive hits
2017-10-04 13:05:18 -04:00
2a554a92e9
r451: changed rep_len mapq heuristic
2017-09-28 14:23:14 -04:00
935a6e6064
r450: differentiate exact repeats via mapq
2017-09-27 23:51:05 -04:00
f611edf6f2
r443: don't filter small cm for split seg
2017-09-26 16:17:58 -04:00
55d1e4f638
r440: better chain filtering for PE reads
2017-09-26 11:03:36 -04:00
9943e5fdd0
backup
2017-09-20 14:35:46 -04:00
03d6894517
backup
2017-09-20 11:47:46 -04:00
11081c6c27
r411: refactored kalloc for clarity
...
The new version is closer to K&R's original implementation.
2017-09-18 19:49:15 -04:00
4d3768bf26
r364: improved the mapq heuristics
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* use repetitive seed lengths, not counts
* compute n_sub to higher accuracy
* use bwa-mem mapq heuristic as a backup
For short single-end reads, minimap2's ROC is not as good as bwa-mem's, but is
close.
2017-09-14 12:37:03 -04:00
47e9d76ca1
further mapq tuning
2017-09-14 10:46:14 -04:00
6a82a21dee
r361: improved mapq for short reads
2017-09-13 15:32:39 -04:00
19d6ec885e
r224: inversion alignment around Z-drop break
2017-07-29 13:09:10 -04:00
254280b8af
r216: a bit cleanup; identical output to r215
2017-07-28 11:54:18 -04:00
a01d758af6
r206: mapq penalize short chains further
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The old code penalized at the log() scale. Now added a linear-scaled factor. If
the chain consists of few minimizers, its quality is really not good.
2017-07-26 11:50:04 -04:00
e9dc1ce2b6
r205: when computing mapq, consider min_chain_sc
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Not doing this was a mistake.
2017-07-26 11:34:14 -04:00
00c6db5073
r203: check more subopt aln if score small
2017-07-25 20:02:44 -04:00
38aa66fa30
r178: fixed integer overflow in mapq calculation
2017-07-16 21:45:39 -04:00
b4280d186f
r176: removed seedcov_ratio; changed default opt
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min_seedcov_ratio is not used
2017-07-12 12:47:46 -04:00
801bc84b01
r169: output more accurate col. 10&11 to PAF
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In r168, col.10 is smaller than what it should be. This confuses miniasm.
2017-07-11 14:09:51 -04:00
782449975d
r168: fixed a bug in long join: a[] not sorted
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Also added length requirement for long join and changed -g in the ava mode
2017-07-09 12:14:20 -04:00
1ac48556ae
r167: long join threshold depends on gap
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also caught a bug for reverse strand join
2017-07-09 10:38:51 -04:00
38b2830e18
r161: filter bad seeds; changed default -g/-r
2017-07-08 13:31:27 -04:00
e07daad7ad
r153: sam primary record not set sometimes
2017-07-03 13:18:57 -04:00
b625247300
r150: mm_sync_regs() doesn't work with negative id
2017-07-03 11:36:34 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
696ebce66e
backup; still buggy
2017-07-03 00:52:00 -04:00
e06c342659
r146: in filtering, drop children if parent out
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This has been causing several segfaults.
2017-07-03 00:28:12 -04:00
632b8638d2
r144: adjust primary aln after cigar
2017-07-02 22:43:02 -04:00
2b45ba7a0b
r143: fixed a segfault and incorrect .parent
2017-07-02 19:56:21 -04:00
74d306a596
fixed bug when retaining 2ndary aln; still buggy
2017-07-02 19:08:30 -04:00
426c2975f6
r126: filter by fraction of seed coverage
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otherwise we may get too many poor overlap mappings.
2017-06-30 22:15:45 -04:00
3a5486325a
r123: fixed a mem leak; more presets
2017-06-30 15:39:05 -04:00
646a746cdc
r122: filter contained aln after DP extension
2017-06-30 15:23:30 -04:00
08a61c3cfc
r119: fixed a bug hidden by a previous bug
2017-06-30 13:27:47 -04:00
1a903486b9
r118: bugfix - regs unsorted before filtering
2017-06-30 12:52:28 -04:00
52b4d8e2c9
r115: set primary tag; still buggy
2017-06-29 23:48:35 -04:00
11167f511b
r112: output z-drop
2017-06-29 22:08:46 -04:00
4cd456b9ba
r108: refactoring, move reg1 routines to hit.c
2017-06-29 19:44:11 -04:00
ecedfe5788
code refactoring for mm_reg1_t
2017-06-29 19:35:38 -04:00
Heng Li