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
...
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
Heng Li
mvdbeek