163fa36ee6
r281: don't open long gaps on query
2017-08-10 15:04:59 -04:00
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
7429b12164
Merge branch 'master' into cdna
2017-08-08 22:00:24 -04:00
9e1125edda
r277: abort if query/-d missing ( #11 )
2017-08-08 21:46:15 -04:00
3dbe23b34e
Merge branch 'dev'
2017-08-08 21:30:32 -04:00
6840370f3c
Release minimap2-2.0 (r275)
2017-08-08 21:16:25 -04:00
7f9f659b6a
r274: CLI option to change max ref gap
2017-08-08 11:39:23 -04:00
1a7d782131
r273: cdna mapping mode for testing
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Differences from the typical mapping mode:
* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
2017-08-08 11:31:49 -04:00
12cea727b8
r238: bugfix to cs - rev sequence not complemented
2017-08-01 10:33:21 -04:00
cd105b47f2
r237: fixed a bug in outputting cs:Z
2017-07-31 14:49:39 -04:00
35f232c3fa
r236: in cs tag, output differences in lowercase
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for easy eyeballing
2017-07-31 12:17:48 -04:00
4c0713ee14
r235: optionally output tag cs in PAF
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cs encodes the query, the reference sequence and CIGAR.
2017-07-31 12:06:49 -04:00
9e09c1ae72
fix self-comparison in index parameter override check
2017-07-30 21:46:25 +03:00
d8d4d29b68
Release minimap2-2.0rc1-r232
2017-07-30 14:32:40 -04:00
1f78e1ee53
r230: code formatting changes only
2017-07-30 12:31:40 -04:00
5934d68772
r229: a new way to prevent out-of-band backtrack
2017-07-29 23:52:30 -04:00
fa99d28d34
r228: reduced unnecessary INV alignment
2017-07-29 20:21:53 -04:00
d08b7a0c51
r227: use local alignment for INV alignment
2017-07-29 17:40:53 -04:00
da3db3c095
r226: only try inv alignment for primary
2017-07-29 14:09:35 -04:00
783ead6f47
r225: removed a debugging line
2017-07-29 13:21:38 -04:00
19d6ec885e
r224: inversion alignment around Z-drop break
2017-07-29 13:09:10 -04:00
5e3eecd6d4
r222: no effective changes
2017-07-29 10:31:46 -04:00
2179e9e24b
r221: output SA in the SAM output
2017-07-28 23:08:39 -04:00
ebbe9c1eb8
r219: fixed a bug caused by skipping tandem seeds
2017-07-28 14:06:56 -04:00
c672690564
r218: increase the frequency of SW slightly
2017-07-28 13:30:42 -04:00
f4fee60188
r217: ignore tandem seeds during alignment
...
This helps a tiny bit.
2017-07-28 12:26:56 -04:00
254280b8af
r216: a bit cleanup; identical output to r215
2017-07-28 11:54:18 -04:00
fc965805f7
r215: bring back a log gap component
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Otherwise chaining may more often break a long gap into several gaps.
2017-07-28 00:17:19 -04:00
2c79580649
r213: more careful solution to wrong seeds
...
a little better, but not good enough!
2017-07-27 13:19:11 -04:00
b927838495
r212: better heuristic to fix wrong seeding
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but not good enough. Will explore more.
2017-07-27 11:24:51 -04:00
371e20cc7c
r211: a better heurstic to reduce false seeds
2017-07-26 23:56:38 -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
f2ef48878a
r202: trim bad chain ends before extension
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This fixes a few more FP long INDELs towards the end of alignments.
2017-07-25 19:53:19 -04:00
21ca564112
r201: fixed a minor chaining issue
...
Chaining looked at the end of a chain, but the end may not be the best. We now
go back to find the max.
2017-07-25 18:26:51 -04:00
215e92ed7b
r200: reduce long gaps in chaining
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Every seed can initiate a chain.
2017-07-25 17:32:54 -04:00
b530ade333
r199: changed to linear gap cost for chaining
...
The old cost doesn't penalize long gaps enough. Will also drop seeds close to
the edge in the next commit.
2017-07-25 15:35:10 -04:00
f81f37fef1
r197: allocate index seq names from kalloc
...
to reduce malloc() overhead.
2017-07-24 19:36:05 -04:00
5c4d040b13
r191: warning if CLI index opt diff from prebuilt
...
Also added index testing API (moved from main.c to index.c)
2017-07-19 10:25:11 -04:00
4aff301ef4
r190: default -k to 15; added -x map-ont
2017-07-19 10:11:14 -04:00
470021fd27
r189: sync with ksw2 (no effective changes)
2017-07-19 09:28:25 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
b9b0b6f49c
r187: fixed non-terminated sam output ( #3 )
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Only happen to unmapped read, with quality, and in the SAM output
2017-07-18 15:20:29 -04:00
495a78e40a
Get documentation ready for release
2017-07-18 11:04:09 -04:00
71e2a97a4c
r180: changed -x asm5 settings
2017-07-18 00:00:36 -04:00
941059292e
r179: changed the preset for assembly alignment
2017-07-17 22:41:46 -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
52caf79395
r175: halved max-chain-skip in the ava mode
2017-07-12 10:42:19 -04:00
Heng Li
Riku Walve