12a5a5fa3c
r669: improved self chain extension ( #10 )
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This has not fully resolved #10 , only alleviated the issue.
2018-01-30 20:05:02 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -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
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
0e42628ef6
r611: document --idx-no-seq; better inv aln
2017-12-08 13:16:18 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -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
a7b38f6900
r562: fixed a severe bug: wrong query start
2017-11-08 22:31:05 -05:00
98ba8928c6
r558: dp_max no less than dp_score
2017-11-08 10:06:10 -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
beeb806829
r526: fixed a bug when HPC is in use
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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
ffd953029f
r519: fixed a severe bug that misses long alns
2017-10-17 15:52:36 -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
e6f525edaf
r512: option to filter poorly aligned reads
2017-10-16 10:38:22 -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
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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
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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
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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
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Still one thing to do: left alignment
2017-10-09 22:02:30 -04:00
1e53610fb4
r493: reduced calling extd2 for ungapped aln
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Still need to improve in case of 3I5M3D
2017-10-09 21:13:34 -04:00
9fea4d16b3
r490: improved short-read extension heuristic
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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
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it doesn't work well
2017-10-08 19:29:09 -04:00
e0baf1ad54
r479: a bit code cleanup
2017-10-05 16:15:14 -04:00
3ff6eda3a4
r473: don't count introns into blen
2017-10-05 14:37:21 -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
645db3350e
Merge branch 'master' into sr
2017-09-20 11:15:14 -04:00
75e6bbc9f6
r421: removed the MM_F_SPLICE_BOTH mode
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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
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--sr disables Z-drop and may come with other heurstics
2017-09-20 10:51:18 -04:00
11081c6c27
r411: refactored kalloc for clarity
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The new version is closer to K&R's original implementation.
2017-09-18 19:49:15 -04:00
0f7455cefa
r365: documented the "sr" preset
2017-09-14 12:57:21 -04:00
d7f2ac1d4f
better parameters for short reads
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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
eccdb3a1ca
r315: added getopt from musl
2017-09-01 20:20:34 +08:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
993a2bb521
r301: separate introns from deletions
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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
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
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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
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -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
Heng Li