f5cfd439ee
r651: incorrectly treat introns as deletions
...
This happened when the last operation during backtracking is an intron.
2018-01-07 19:42:50 -05:00
dc9e3dcf4a
r639: changed -O/-E validation
2017-12-30 20:39:29 -05:00
cc75c12905
r638: disabled scoring checking
...
I haven't figured out the exact bounds...
2017-12-30 07:50:40 -05:00
e420b17496
r629: API to construct index from strings
2017-12-18 22:29:46 -05:00
ab345e600b
r626: function to check incorrect scoring system
2017-12-13 12:23:43 -05:00
d003a00d71
r625: HPC sketch still has one minor issue
2017-12-13 09:40:42 -05:00
eb819c29e8
Release minimap2-2.6 (r623)
2017-12-12 11:09:59 -05:00
fb630de40a
r622: fixed bug in sdust due to recent refactor
2017-12-11 15:32:28 -05:00
43960a8ca7
r621: --print-qname also shows kalloc status
2017-12-11 12:30:08 -05:00
f6608fe99c
r620: revamped thread-local memory management
...
* Don't preallocate sdust_buf or minizer list. kalloc should be fast enough -
benchmarks needed to confirm.
* Fixed a memory leak caused by divergence estimate (post v2.5)
* Reset the kalloc buffer after mapping a long query. This reduces peak memory
when large chunks of memory are allocated, at the cost of performance, though.
2017-12-11 12:11:10 -05:00
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
824712a4ee
r617: removed some unused code
2017-12-10 17:54:50 -05:00
98a999fe44
r611: added pseudocount when est divergence
2017-12-08 12:57:57 -05:00
fec7bd713f
r610: warning if db sequence is 0-lengthed ( #69 )
2017-12-07 21:05:39 -05:00
2f693e8ca4
r609: bugfix - SDUST masking not working
2017-12-07 11:45:38 -05:00
704ff9f4c6
r607: estimate sequence divergence
...
Currently using the simplest method. There may be a more accurate estimate.
2017-12-06 16:14:39 -05:00
68c63f2d68
r606: fixed a sketch bug for long 256bp k-mer
...
sketch() writes {-1,-1} to the output array.
2017-12-06 16:13:29 -05:00
984f7846c0
r601: bugfix - a similar issue to r600
...
This bug unsets the alignment score of suboptimal alignments.
2017-11-30 11:51:34 -05:00
af1d6afba9
r600: bugfix - missing secondary alignments ( #71 )
...
This should very rarely happen to typical data, but has a higher chance in
artifactual data.
2017-11-30 11:34:10 -05:00
131cfc6938
r574: build index without sequences
2017-11-11 21:38:38 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
3b518271ee
Release minimap2-2.5 (r572)
2017-11-11 11:29:28 -05:00
d7a31e40e6
r569: last commit is buggy
2017-11-09 23:20:41 -05:00
dd18cd75de
r568: revert - don't take max(dp_max, dp_score)
2017-11-09 23:12:48 -05:00
99a2709913
r567: minor change to #56
2017-11-09 19:17:45 -05:00
1cb0bf4bef
Implement -Y for soft clipping of supp. alignments
...
I tried to base this on bwa-mem and it seems to work for sam alignments.
2017-11-09 19:22:36 +01:00
a7b38f6900
r562: fixed a severe bug: wrong query start
2017-11-08 22:31:05 -05:00
e896c9ec05
r559: prefer a chain involving more segments
2017-11-08 13:22:16 -05:00
98ba8928c6
r558: dp_max no less than dp_score
2017-11-08 10:06:10 -05:00
b24d68ae9f
r557: fixed another mapq underestimate
...
When a chain is split during base-level alignment, its chaining score is
reduced. However, the chaining score of its suboptimal chain remains the same.
This leads to underestimated mapping quality.
2017-11-07 23:20:49 -05:00
65deedfa96
r556: bugfix - underestimate mapq for split aln
2017-11-07 22:37:12 -05:00
21a46ba652
Release minimap2-2.4 (r555)
2017-11-06 12:54:02 -05:00
fa5a645ca5
r552: fixed a tiny typo on struct packing
...
The old packing wastes memory, thought very small.
2017-11-05 08:27:26 -05:00
a3f0aa1d5b
r550: fixed -L issues with secondary and supp aln
2017-11-04 12:13:38 -04:00
22290db3e4
r546: minor mapQ tuning
2017-11-01 13:20:39 -04:00
cd24dc8834
r545: removed option -i, not working well
2017-10-31 22:23:27 -04:00
b8e758df0f
r544: increased PE mapQ
2017-10-31 16:55:02 -04:00
311fa90030
r543: applied some sr mapq changes to long reads
2017-10-31 15:24:05 -04:00
fb8a1b5536
r542: tuning mapQ calculation
2017-10-31 14:25:09 -04:00
285eb0da05
r540: removed a buggy debugging line
2017-10-29 00:02:41 -04:00
192217a10c
r539: use --splice-flank=yes by default
...
In human/mouse, the GTr..yAG pattern occurs to 91/92% of all GT-AG introns.
Modeling r..y clearly leads to higher accuracy. However, in SIRV, this
percentage is reduced to ~60%. The default "--splice --splice-flank=yes"
leads to lower accuracy. If someone benchmark minimap2 on SIRV, this would be
bad, but minimap2 is developed for practical applications, not for benchmarks.
I will live with that.
2017-10-28 22:29:55 -04:00
f22a94e868
r538: fixed a long existing bug in HPC k-mer ( #47 )
...
This bug may lead to a wrong minimizer when a HPC k-mer is longer than 256bp.
When there is a seed match involving this wrong HPC k-mer, the correct seed
sequences do not match in fact. This violates the assumption in align.c and
subsequently causes a segfault, which is what #47 has caught. This bug lurked
in the earliest piece of code and affected all released minimap2 versions so
far. It is extremely rare and does not affect the prebuilt GRCh37/38 indices.
2017-10-28 19:21:10 -04:00
79b0caca95
r537: model the next base to GT/AG
...
[PMID:18688272] shows that the base following GT tends to be A or G (i.e. R) in
both human and yeast, and that the base preceeding AG tends to be C or T (i.e.
Y). In the new model, we pay no cost to GTr..yAG, but we pay half of the cost
if there is no r or y. This improves the junction accuracy when mapping to
human and mouse and decreases the accuacy when mapping to SIRV. My guess is
that SIRV does not honor this trend. Need to investigate in future.
Also in this commit, --cost-non-gt-ag is aliased to -C. The default is changed
to 9 instead of 5. I also added --splice-flank to enable the above model. This
may become the default once I confirm my hypothesis on SIRV.
2017-10-28 00:25:01 -04:00
afc2f2e84b
r536: removed an unnecessary assert()
2017-10-24 21:08:54 -04:00
d4b5dfc297
r533: added --no-pairing
...
to prevent the use of any pairing information for paired-end reads.
2017-10-23 14:09:32 -04:00
306e4541f8
Released minimap2-2.3 (r531)
2017-10-22 23:13:35 -04:00
beeb806829
r526: fixed a bug when HPC is in use
...
It happened when the query HPC minimizer is longer than the reference HPC
minimizer close to the beginning of a contig. We may get a negative coordinate,
which causes an assertion failure.
2017-10-21 19:54:04 -04:00
be7f3c4ffe
r525: fixed a bug in chaining; handle ovlp ends
2017-10-20 21:34:52 -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
15ed0712c2
r523: fixed a performance bug in ksw2_ll
...
Wont' affect accuracy.
2017-10-20 13:00:10 -04:00
4683da2455
r520: added option -L to write long cigar to CG
2017-10-17 17:32:44 -04:00
ffd953029f
r519: fixed a severe bug that misses long alns
2017-10-17 15:52:36 -04:00
04cf4ebf5e
r518: increased the default -K to 500M
...
This helps multi-thread performance for ultra-long reads.
2017-10-17 13:21:29 -04:00
25ffd72690
r517: replaced --print-2nd with --secondary
2017-10-17 11:41:56 -04:00
aa2d9d4e1b
r516: throw a warning if -N0 is used
2017-10-16 14:55:35 -04:00
addb61bcb2
r515: more conservative hit exclusion
...
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
...
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
858213d513
r511: fixed wrong primary sam record
2017-10-12 23:02:18 -04:00
dea3b60918
r510: fixed an off-by-1 bug for unmapped mate
2017-10-12 17:31:13 -04:00
7c555f9b7e
r508: use two I/O threads for mapping
...
-x sr applies this option by default
2017-10-12 14:56:01 -04:00
2801ed9b4b
r507: -K not working as is intended ( #36 )
2017-10-12 14:16:05 -04:00
ce06188203
r506: fixed a memory leak
2017-10-12 10:12:22 -04:00
9862a75cd3
r505: a bit code simplification
2017-10-11 21:54:32 -04:00
3073f4a758
r504: better heuristics to reduce excessive ext
2017-10-11 21:42:11 -04:00
9364bc64d7
r501: added end_bonus to extz2
2017-10-11 09:39:41 -04:00
65abdb8f3c
r500: temporarily disabled region trunc
...
because it is causing other problems.
2017-10-11 00:16:04 -04:00
7345621759
r499: end bonus working; DP region needs improve!
2017-10-11 00:14:25 -04:00
ca632f907b
r498: fixed a bug when merging like "4I5I"
2017-10-10 21:22:37 -04:00
6c78a980b6
r497: the previous change not working at the ends
2017-10-10 17:32:28 -04:00
c217eecdb7
r496: avoid DP extending into another chain
...
When deciding the region for DP, exclude regions in the adjacent chain
2017-10-10 17:25:12 -04:00
13b66aad4d
r495: fix impropriate CIGAR
...
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
46fa520db9
r494: simpler and better SR gap filling
...
Still one thing to do: left alignment
2017-10-09 22:02:30 -04:00
1e53610fb4
r493: reduced calling extd2 for ungapped aln
...
Still need to improve in case of 3I5M3D
2017-10-09 21:13:34 -04:00
9396d9e11b
r452: typo in the last commit
2017-10-09 10:05:32 -04:00
198849a716
r491: an ambiguous base costs the same as gap ext
2017-10-09 09:59:42 -04:00
9fea4d16b3
r490: improved short-read extension heuristic
...
Now we find the best scoring ungapped seeded segment and then extend from it.
There is no gap filling for short reads.
2017-10-08 21:36:34 -04:00
f9415628a8
r489: don't use approximate zdrop
...
it doesn't work well
2017-10-08 19:29:09 -04:00
61e56c941d
r488: parameter to control max fragment length
2017-10-07 23:54:32 -04:00
f150257a0d
r487: demote "map10k"; improved README
2017-10-07 19:19:40 -04:00
bf2d4f7aec
r486: treat "U" as "T" for RNA reads ( #33 )
2017-10-07 18:53:25 -04:00
c6384ed2c8
r482: increased short-read bandwidth to 100
...
This has very minor effect on speed.
2017-10-06 10:20:32 -04:00
e0baf1ad54
r479: a bit code cleanup
2017-10-05 16:15:14 -04:00
f266092699
r478: simplied useless code, a tiny bit
2017-10-05 15:56:00 -04:00
9c5767f9ed
r477: renamed multi_seg to frag_mode
2017-10-05 15:48:17 -04:00
ae2adf04d4
r476: multi-file fragment mode working
2017-10-05 15:39:26 -04:00
b839758335
r475: added --cs=none; updated manpage
2017-10-05 15:27:37 -04:00
f4a5d3a692
r474: replaced -S and --cs-no-equal with --cs
2017-10-05 15:03:03 -04:00
3ff6eda3a4
r473: don't count introns into blen
2017-10-05 14:37:21 -04:00
1a90bc8603
r472: fixed a bug when printing MAPQ/CIGAR
2017-10-05 12:46:11 -04:00
abf2a90363
r471: all SAM features implemented; more tests!
2017-10-05 12:37:30 -04:00
7cc4f6f965
r469: first step towards PE SAM
2017-10-05 10:38:09 -04:00
16e6e589a8
r468: replaced ^ with ~ in cs
2017-10-04 22:17:12 -04:00
9aba11769c
r467: added : (equal length) and ^ (intron) ops
2017-10-04 21:55:37 -04:00
7d50e646dd
r466: detect multi-part index more smartly
...
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
2017-10-04 17:32:58 -04:00
1554149158
r465: apply option -x before other options
2017-10-04 13:52:28 -04:00
19c39e704f
r464: fixed a bug in pairing, due to randomization
2017-10-04 13:37:40 -04:00
2581c44a21
r463: optionally disable secondary hits
2017-10-04 13:24:41 -04:00
5babf41a38
r462: SAM primary flag not properly set
2017-10-04 13:11:29 -04:00
2a1e738a94
r461: randomize repetitive hits
2017-10-04 13:05:18 -04:00
cf55c84056
r460: added option --no-long-join
2017-10-04 12:08:44 -04:00
841763ec24
Merge branch 'master' into sr
2017-10-04 11:42:44 -04:00
95eb1dec36
r458: fixed wrong chr for inversion aln ( #30 )
2017-10-04 11:32:06 -04:00
0fd0f2aed1
r457: fixed a bug on parsing -f
2017-09-30 00:00:44 -04:00
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
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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
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
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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
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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
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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
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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
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to reduce malloc() overhead.
2017-07-24 19:36:05 -04:00
5c4d040b13
r191: warning if CLI index opt diff from prebuilt
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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
eeeb2ffb68
r174: make max-chain-skip work
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The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
2017-07-12 10:08:06 -04:00
33451aba45
r173: changed the debugging output format
2017-07-11 15:23:28 -04:00
cfa083a98b
r172: separated PacBio and ONT read overlapping
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HPC k-mer works better for PacBio, but worse for ONT. Interesting...
2017-07-11 15:12:35 -04:00
7598809577
r171: reduced log gap cost at chaining
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The cost is so large that it discards too many valid seeds without HPC k-mers.
This change may introduce false long gaps to reference mapping. We have another
mechanism mm_filter_bad_seeds() to protect against this. In addition, minimap2
is not that bad to have long gaps. Some other aligners are worse.
Still need tuning in future.
2017-07-11 14:57:49 -04:00
826c8ba892
r170: added a debugging flag
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something wrong with chaining
2017-07-11 14:47:35 -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
4ee3202539
r164: unmapped read not properly flagged
2017-07-08 18:16:18 -04:00
42846ce65d
r163: reduced long join score requirement
...
because the chaining score is generally smaller with the last few commits.
2017-07-08 15:51:52 -04:00
3f6a0b0b5c
r162: improved chaining accuracy
2017-07-08 14:29:36 -04:00
38b2830e18
r161: filter bad seeds; changed default -g/-r
2017-07-08 13:31:27 -04:00
1fee5f8edc
r160: -O and -E accept two numbers
2017-07-08 11:34:52 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
9823317e8f
r158: optionally ignore base quality
2017-07-05 18:23:50 -04:00
e07daad7ad
r153: sam primary record not set sometimes
2017-07-03 13:18:57 -04:00
a94bc31311
r151: documentations
2017-07-03 12:11:07 -04:00
b625247300
r150: mm_sync_regs() doesn't work with negative id
2017-07-03 11:36:34 -04:00
53c4bf5e4f
r149: introduced debugging flags on CLI
2017-07-03 11:02:32 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
Heng Li
mvdbeek
Simon Harris
Stefan von Deylen
Riku Walve