eba237f39d
r910: meaningful error message ( #320 )
...
when minimap2 fails to create temporary files
2019-01-29 10:29:27 -05:00
597212b9f3
r908: added an assertion to detect a potential bug
...
as in #311
2019-01-23 11:18:50 -05:00
48e230f40d
r906: de tag is wrongly calculated given "N"
...
Resolves #309
2019-01-11 19:39:09 -05:00
c404f49569
Release minimap2-2.15 (r905)
2019-01-10 12:34:45 -05:00
cf2bae6e9b
r904: fixed a corner-case segfault. Resolves #307 .
2019-01-10 09:57:05 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
2c52364527
r892: avoid de:f:0.0000
2018-11-24 21:54:28 -05:00
128476efc9
r891: compute gap-compressed divergence
2018-11-24 21:50:49 -05:00
1b3a6a0fe5
r890: removed "register" ( #261 )
2018-11-19 13:57:31 -05:00
83a8ee7038
r888: fixed incorrect CIGAR when --eqx in use
...
This was caused by mm_fix_cigar() which may change query/target offset in very
rare cases. Generating EQX has to beware of this change.
Resolves #266
2018-11-18 14:22:29 -05:00
91f548b497
r886: fixed two minor typos
...
Resolves #264
Resolves #265
2018-11-08 12:04:14 -05:00
6596c63dcd
r884: for C++ compatibility ( #261 )
2018-11-06 22:07:11 -05:00
59f23f7579
Release minimap2-2.14 (r883)
2018-11-06 00:03:16 -05:00
5e55e397e9
r882: guard against -E0 ( #263 )
2018-11-05 23:36:12 -05:00
88c421e8de
r881: a recent change reduces sr accuracy
2018-11-05 22:03:59 -05:00
3db5bfe6e5
r880: fixed false wrong FASTA/Q alert
2018-11-05 20:52:07 -05:00
1ede8ca170
r877: renamed cap-sw-mat to cap-sw-mem
2018-11-05 11:46:38 -05:00
13981404e2
r876: skip DP if taking too much RAM ( #259 )
2018-11-05 11:43:10 -05:00
fd64dd26f6
r875: warn given incorrect FASTA/Q
...
resolves #252
resolves #255
2018-11-05 10:02:44 -05:00
24df95e4b8
r874: don't call x86_simd() so often
...
This takes a few percent of time in profiler.
2018-11-05 09:20:35 -05:00
a8ee48c2ce
r873: comforming to C99/C11; resolves #261
2018-11-05 08:25:07 -05:00
42baf287a4
r866: fixed a typo; resolves #262
2018-10-30 09:11:55 -04:00
9ed56b4a25
r860: MD/cs not working with --eqx
2018-10-26 23:23:53 -04:00
377c7099a8
r858: fixed a bug; resolves #254
2018-10-22 22:47:11 -04:00
7b0a49732e
r856: wrongly reported for an unrecognized option
...
Resolved #250
2018-10-19 20:07:14 -04:00
d04ac068fd
r852: a minor when large --end-bonus is in use
...
We may use a large --end-bonus to mimic end-to-end alignment. In the short-read
mode, the candidate alignment region may be out of the band, which leads to
truncated alignment.
2018-10-15 21:28:27 -04:00
5d5d392c02
Release minimap2-2.13 (r850)
2018-10-11 13:18:31 -04:00
170863e553
r849: option -P doesn't work
...
I don't know why I haven't found it at the beginning.
2018-10-04 16:11:59 -04:00
97f97306a4
r847: guard against -N0
2018-09-27 15:13:44 -04:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
c57b59f02f
r845: log peak memory
2018-09-23 20:27:49 -04:00
c63a33904f
r836: fixed an integer overflow
...
Forgot this one.
2018-09-14 23:29:31 -04:00
70b0fede64
r835: improved help message. Resolved #232
2018-09-14 22:29:25 -04:00
7d80d6de4a
r832: fixed outdated -L. Resolved #231 and #233
2018-09-14 22:21:33 -04:00
7998fe9906
r829: replaced musl's getopt with ketopt
2018-09-01 21:18:02 -04:00
3a119d606f
r828: --MD to support spliced alignment
2018-08-22 10:47:45 -04:00
a5eafb75f9
Release minimap2-2.12 (r827)
2018-08-06 12:44:39 -04:00
b0f39a1a61
r823: mappy to index a single sequence
2018-08-05 20:57:05 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
b32296e18f
r821: fixed memory when -y is used
2018-07-31 15:14:37 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
830da7fa27
r814: resumed versioning
2018-07-15 11:48:14 -04:00
a655cbef86
print SAM header; remove tmp files
2018-07-15 11:03:18 -04:00
e5277dbf5c
code backup
2018-07-14 22:52:36 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
0517972d02
Release minimap2-2.11 (r797)
2018-06-21 00:04:08 -04:00
d46e68e6ad
r796: don't use ssize_t
2018-06-20 12:45:27 -04:00
2584a4149a
r295: use -r2000 for ava-ont, NOT for ava-pb
2018-06-20 12:24:43 -04:00
66674afd09
r794: fixed a bug in seed filtering
2018-06-20 10:26:29 -04:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
3573784b4d
r782: no mask a chain having long ref ovlp ( #155 )
2018-05-30 13:53:45 -04:00
872f300955
r781: fixed the buggy heapmerge ( resolves #166 )
2018-05-30 11:55:14 -04:00
9f4309c376
r777: avoid skipping too many seeds
2018-05-11 10:25:18 -04:00
881b4ca3a2
r774: Merge branch 'hot-fix' into fix-long-gap
2018-05-11 10:02:17 -04:00
10c6dd2551
r773: fixed an integer overflow
2018-05-11 10:01:23 -04:00
7ec6721c44
r772: option -Y not working
2018-05-11 10:00:11 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
759f8e4ac9
r769: filter out seeds breaking long gaps
2018-04-24 15:37:37 -04:00
aef7b0744c
r768: shortened preset; added dv tag ( #25 )
...
Also added asm20 to command line help (#151 )
2018-04-24 12:48:54 -04:00
372c90ceb5
r764: fixed incorrect inversion mapq ( #148 )
2018-04-10 09:11:49 -04:00
ee4cd089f7
r763: fine control long join flank len ( #128 )
2018-03-29 14:16:58 -04:00
2d7ec75d50
Release minimap2-2.10 (r761)
2018-03-27 11:45:44 -04:00
5ef9580b17
r753: change bandwidth in ava-ont to 2000bp
2018-03-23 10:15:23 -04:00
08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
8766d286df
r751: optionally output MD ( #118 )
2018-03-22 14:15:33 -04:00
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
18659118cd
r749: don't print version etc at low verbose
2018-03-22 11:10:55 -04:00
d1050f4eaf
r748: optionally to use system getopt() ( #134 )
2018-03-19 11:18:26 -04:00
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
eeb314edd6
Release minimap2-2.9 (r720)
2018-02-24 09:31:09 -05:00
83c57a9d98
r719: fixed bad memory access
2018-02-23 17:27:41 -05:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
a0d62519c1
r710: fixed incorrect inversion coordinate ( #112 )
2018-02-15 14:23:42 -05:00
1372977a37
r708: implemented double Z-drop thresholds ( #112 )
...
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 ).
2018-02-15 10:50:49 -05:00
c0e0d5d84b
r707: bugfix for inversions on rev strand ( #112 )
2018-02-14 14:09:03 -05:00
b328795051
r706: don't segfault upon wrong FASTA/Q ( #111 )
...
The lack of robustness cost me several hours to identify.
2018-02-13 10:00:22 -05:00
7ef5490884
r703: added --max-clip-ratio
...
still testing the option
2018-02-12 13:29:18 -05:00
a8d476c6ad
r686: end seed trimming don't go over long join
2018-02-06 11:31:32 -05:00
29b4a1786c
r685: tune end seed filter again
2018-02-05 11:48:22 -05:00
dbf284b2d9
r684: separate end score from min_chain_score
2018-02-05 11:40:38 -05:00
35d3e064bf
r677: reduce the change of missing hits
...
that are close to end of alignments. It is still possible to create examples
that fail the heuristic.
2018-02-02 10:35:33 -05:00
53ce317e59
Release minimap2-2.8 (r672)
2018-02-01 12:50:20 -05:00
da6947cfa3
r671: cleanup command line options
2018-01-31 13:59:52 -05:00
46d6349af4
r670: added PE support to mappy
...
and minor code cleanup
2018-01-31 11:33:08 -05:00
12a5a5fa3c
r669: improved self chain extension ( #10 )
...
This has not fully resolved #10 , only alleviated the issue.
2018-01-30 20:05:02 -05:00
43bfa6199d
r667: warn if one query file has fewer records #92
2018-01-28 17:36:21 -05:00
72b9b0e3b6
r666: report if >=3 query files in SR mode #92
2018-01-28 17:15:57 -05:00
d676a5314b
r664: use --heat-sort for sr by default
2018-01-26 12:25:42 -05:00
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
543fa12e68
r659: for C++ compatibility
2018-01-19 10:40:18 -05:00
af1a871270
r658: gives a warning if -N0 is used
2018-01-19 08:33:20 -05:00
2b71181a37
r657: check -p ( #96 )
...
Well, in principle, every option should be checked. Will do when someone raise
issues...
2018-01-19 01:03:38 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -05:00
eecc06086f
Released minimap2-2.7 (r654)
2018-01-09 13:16:00 -05:00
dfea113f28
r653: the last change may write "N" wrongly
2018-01-08 11:33:53 -05:00
f5cfd439ee
r651: incorrectly treat introns as deletions
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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
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sketch() writes {-1,-1} to the output array.
2017-12-06 16:13:29 -05:00
984f7846c0
r601: bugfix - a similar issue to r600
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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
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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
Heng Li
mvdbeek