ee9b2773a8
r456: min chain score should >k-mer length
...
or chain_dp() wastes time on unnecessarily sorting chains with one k-mer.
2017-09-29 22:33:55 -04:00
340483821e
r455: set max_occ on command line
2017-09-29 22:18:43 -04:00
04fb2c2ec0
r454: rechain with higher max_occ if no good chain
2017-09-29 19:24:32 -04:00
0d4ecd19ee
r453: avoid duplicated strcmp() for ava
2017-09-28 15:52:05 -04:00
0c63325985
r452: fixed - -G not working with -x sr
2017-09-28 14:28:12 -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
8301222174
r448: fixed a bug when computing PE quality
2017-09-27 21:54:07 -04:00
7e0d70bfd3
r445: pair coordinate adjustment working
...
Next: mapq adjustment, which will be tricky...
2017-09-27 15:38:18 -04:00
a349d85280
r444: changed the way orientation is specified
...
The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.
2017-09-27 12:33:10 -04:00
f611edf6f2
r443: don't filter small cm for split seg
2017-09-26 16:17:58 -04:00
1b1dd0cd57
r442: default max_gap to 200 in the sr mode
2017-09-26 13:31:01 -04:00
55d1e4f638
r440: better chain filtering for PE reads
2017-09-26 11:03:36 -04:00
64c0ad6b35
r439: use splice-like chain gap cost between segs
...
This improves accuracy
2017-09-25 16:04:38 -04:00
9538c985aa
r438: fixed a rare case that leads to missing hits
...
It is a bug in chaining.
2017-09-25 14:59:34 -04:00
8f25cfa36e
r437: fixed uninialized memory on rep_len
2017-09-25 14:22:45 -04:00
81008dd371
r436: working on short reads
...
The result is mixed - lots of room for tuning
2017-09-25 14:06:29 -04:00
3bb66e1ed3
multi-seg working on toy examples
2017-09-25 13:42:04 -04:00
5b39a1b34b
Merge branch 'master' into sr
2017-09-20 12:24:08 -04:00
e3b5802b2e
r424: reduce memory for long query seqs
2017-09-20 12:22:13 -04:00
645db3350e
Merge branch 'master' into sr
2017-09-20 11:15:14 -04:00
75e6bbc9f6
r421: removed the MM_F_SPLICE_BOTH mode
...
In the default splice mode, minimap2 applies two rounds of spliced alignment:
first assuming GT-AG to be the splice signal across all splicing sites and then
assuming CT-AC to be the signal. This is the idea strategy.
In the MM_F_SPLICE_BOTH mode, minimap2 applies one round of spliced alignment,
assuming GT-AG and CT-AC to be the splice signals AT THE SAME TIME. This will
be faster but less accurate. I don't think anyone would like to run minimap2 in
this mode, so I am removing it for clarity.
2017-09-20 11:11:53 -04:00
7a9b4db874
replaced --approx-ext with --sr
...
--sr disables Z-drop and may come with other heurstics
2017-09-20 10:51:18 -04:00
b99c22840f
r414: avoid assertion failure for 0-length reads
2017-09-19 22:21:27 -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
ea5a0cd17d
Release minimap2-2.2 (r409)
2017-09-17 20:08:47 -04:00
e9c57f6d8b
r402: exposed kseq (for API in mappy later)
2017-09-17 13:09:16 -04:00
c07f9f9a49
r372: default mm_verbose to 1, and change in main
2017-09-16 09:14:34 -04:00
14b853499f
r369: updated example with the latest API
2017-09-14 22:44:10 -04:00
75ff7ceec5
r368: API documentation
2017-09-14 22:23:04 -04:00
e2823d4aee
r367: index reader optionally writes index
2017-09-14 21:18:13 -04:00
eb00521d9b
redesigned indexing and option APIs
2017-09-14 17:02:01 -04:00
0f7455cefa
r365: documented the "sr" preset
2017-09-14 12:57:21 -04:00
4d3768bf26
r364: improved the mapq heuristics
...
* 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
f4a8766283
r362: fixed overestimated chaining score
...
Caused by ilog2_32(0)=-1. This bug was fixed once and reoccurred as I was
tuning the score function but forgot to apply the fix.
2017-09-14 10:15:22 -04:00
6a82a21dee
r361: improved mapq for short reads
2017-09-13 15:32:39 -04:00
3c91d652dd
r360: allow to set integer max occ
2017-09-13 11:37:00 -04:00
d7f2ac1d4f
better parameters for short reads
...
It turns out the key problem is not the minimizer density. It is the max
occurrence that tends to affect results more, especially sensitivity. There is
still lots of work to do, but for now, it seems a good start.
2017-09-12 16:11:23 -04:00
eea9e851d8
Merge branch 'dev' into short
2017-09-11 09:32:28 -04:00
c7c3585531
r347: merged mm_map_frag() into mm_map()
...
mm_map_frag() was separated due to an earlier design that has been rejected.
2017-09-10 15:02:55 -04:00
87a278d06a
Merge branch 'dev' into short
2017-09-09 08:49:58 -04:00
f422175e4e
r344: avoid unnecessary refName retrieval
2017-09-08 22:44:14 -04:00
709b6ec1f1
increase seed occurrences
2017-09-08 22:42:39 -04:00
0031158936
Merge branch 'master' into short
2017-09-07 11:41:32 -04:00
ef3f7ea2f2
Release minimap2-2.1.1 (r341)
2017-09-06 13:46:51 -04:00
8b9f2aaf04
r339: improved SIMD detection
...
old code does not check AVX2
2017-09-05 13:10:30 -04:00
46e8b6a4f9
r338: portable CPU dispatch, which is the default
...
working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
3c997ca016
r337: support CPU dispatch for gcc-4.8+
...
using __builtin_cpu_supports()
2017-09-03 14:29:49 -04:00
f9ccc522cd
Merge branch 'master' into short
2017-09-03 11:58:15 -04:00
101b8bb97d
r335: report an error if query can't be opened
2017-09-03 11:54:38 -04:00
0a3ebdc916
for better windows compatibility
2017-09-02 17:52:33 -04:00
743d26eab0
Merge pull request #20 from nanoporetech/msvc14
...
ONT source code changes to compile with MSVC 14
2017-09-02 14:35:02 -07:00
62535ecd7f
Merge branch 'dev'
2017-09-01 10:06:21 -07:00
4db1c0295c
Fixed segfault caused when reading from index file
2017-09-01 15:48:59 +01:00
d4074874ee
r316: get rid of a harmless gcc warning
2017-09-01 20:25:27 +08:00
eccdb3a1ca
r315: added getopt from musl
2017-09-01 20:20:34 +08:00
a3c3db6b9b
ONT source code changes to compile with MSVC 14
2017-08-30 16:25:20 +01:00
c4080aaf7e
Merge branch 'master' into short
2017-08-28 07:02:22 +08:00
bf8246f872
Release minimap2-2.1-r311
2017-08-25 13:35:55 +08:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
993a2bb521
r301: separate introns from deletions
...
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
2017-08-18 15:31:15 +08:00
64c1389e1a
Merge branch 'master' into splice
2017-08-17 23:39:27 +08:00
81cff97208
r299: support -h: output to stdout; return 0
2017-08-17 23:38:31 +08:00
bbb37d95f2
support inserting RG lines
2017-08-17 23:34:09 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
b5f5929bf9
r296: expose splicing related options to CLI
2017-08-13 21:37:51 -04:00
28f86688ab
r295: gap closure from the middle of non-HPC k
...
This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
2017-08-12 23:48:43 -04:00
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
53b3265d84
r290: in techrep, explain spliced alignment
2017-08-12 15:40:49 -04:00
a23df2dc91
r289: changed CLI help only
2017-08-12 12:40:07 -04:00
5a74088b74
r288: changed max intron length to 200k
2017-08-12 12:39:21 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
0f4c823b0c
r286: ignore introns when computing max seg score
2017-08-12 10:58:16 -04:00
a99358bc3d
r282: reduced intron cost; added eval script
2017-08-11 00:06:01 -04:00
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
...
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
079ec0d283
r271: added "short" preset; for testing only
2017-08-07 15:30:05 -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
...
for easy eyeballing
2017-07-31 12:17:48 -04:00
4c0713ee14
r235: optionally output tag cs in PAF
...
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
Heng Li
Simon Harris
Stefan von Deylen
Riku Walve