f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
9dceae59a0
r972: renamed --alt-diff to --alt-drop
2020-01-21 10:33:39 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
d2e14705e7
r968: allow large mini_batch; resolves #491
2020-01-18 12:24:44 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
c2aec88b84
r938: added --sam-hit-only; resolved #377
2019-04-30 22:40:36 -04:00
97f67a2a0a
r937: enlarge mm_mapopt_t::flag to 64 bits
2019-04-30 22:30:32 -04:00
49c6d83a8e
r934: --junc-bed to read BED12
2019-04-28 20:12:28 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
13981404e2
r876: skip DP if taking too much RAM ( #259 )
2018-11-05 11:43:10 -05:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
3545e35a42
pairing in the split-idx mode
2018-07-14 23:43:34 -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
57f37551f8
expose mm_idx_is_idx, mm_idx_load and mm_idx_dump
2018-06-19 14:46:05 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
ee4cd089f7
r763: fine control long join flank len ( #128 )
2018-03-29 14:16:58 -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
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -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
7ef5490884
r703: added --max-clip-ratio
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still testing the option
2018-02-12 13:29:18 -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
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
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -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
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
704ff9f4c6
r607: estimate sequence divergence
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Currently using the simplest method. There may be a more accurate estimate.
2017-12-06 16:14:39 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
1cb0bf4bef
Implement -Y for soft clipping of supp. alignments
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I tried to base this on bwa-mem and it seems to work for sam alignments.
2017-11-09 19:22:36 +01:00
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
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
cd24dc8834
r545: removed option -i, not working well
2017-10-31 22:23:27 -04:00
79b0caca95
r537: model the next base to GT/AG
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[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
d4b5dfc297
r533: added --no-pairing
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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
4683da2455
r520: added option -L to write long cigar to CG
2017-10-17 17:32:44 -04:00
adf6cd7f52
r513: merged pre- and post-cigar blen and mlen
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This saves a bit memory and is cleaner.
2017-10-16 10:55:18 -04:00
Heng Li
Ilya Kolpakov
mvdbeek