Heng Li
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
Heng Li
a655cbef86
print SAM header; remove tmp files
2018-07-15 11:03:18 -04:00
Heng Li
4b707aac92
working with toy examples
2018-07-15 10:55:00 -04:00
Heng Li
3545e35a42
pairing in the split-idx mode
2018-07-14 23:43:34 -04:00
Heng Li
e5277dbf5c
code backup
2018-07-14 22:52:36 -04:00
Heng Li
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
Heng Li
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
Heng Li
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
Heng Li
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
Heng Li
3573784b4d
r782: no mask a chain having long ref ovlp ( #155 )
2018-05-30 13:53:45 -04:00
Heng Li
872f300955
r781: fixed the buggy heapmerge ( resolves #166 )
2018-05-30 11:55:14 -04:00
Heng Li
08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
Heng Li
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
Heng Li
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
Heng Li
da6947cfa3
r671: cleanup command line options
2018-01-31 13:59:52 -05:00
Heng Li
46d6349af4
r670: added PE support to mappy
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and minor code cleanup
2018-01-31 11:33:08 -05:00
Heng Li
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
Heng Li
dfc78b39d3
refactor the old sorting
2018-01-26 09:37:48 -05:00
Heng Li
7b57c9a619
heap sort working on MT
2018-01-26 09:21:45 -05:00
Heng Li
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
Heng Li
dd18307e66
code backup
2018-01-25 21:52:49 -05:00
Heng Li
af1a871270
r658: gives a warning if -N0 is used
2018-01-19 08:33:20 -05:00
Heng Li
2b71181a37
r657: check -p ( #96 )
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Well, in principle, every option should be checked. Will do when someone raise
issues...
2018-01-19 01:03:38 -05:00
Heng Li
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -05:00
Heng Li
dc9e3dcf4a
r639: changed -O/-E validation
2017-12-30 20:39:29 -05:00
Heng Li
cc75c12905
r638: disabled scoring checking
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I haven't figured out the exact bounds...
2017-12-30 07:50:40 -05:00
Heng Li
ab345e600b
r626: function to check incorrect scoring system
2017-12-13 12:23:43 -05:00
Heng Li
43960a8ca7
r621: --print-qname also shows kalloc status
2017-12-11 12:30:08 -05:00
Heng Li
f6608fe99c
r620: revamped thread-local memory management
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* 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
Heng Li
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
Heng Li
824712a4ee
r617: removed some unused code
2017-12-10 17:54:50 -05:00
Heng Li
98a999fe44
r611: added pseudocount when est divergence
2017-12-08 12:57:57 -05:00
Heng Li
2f693e8ca4
r609: bugfix - SDUST masking not working
2017-12-07 11:45:38 -05:00
Heng Li
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
Heng Li
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
Heng Li
cd24dc8834
r545: removed option -i, not working well
2017-10-31 22:23:27 -04:00
Heng Li
fb8a1b5536
r542: tuning mapQ calculation
2017-10-31 14:25:09 -04:00
Heng Li
192217a10c
r539: use --splice-flank=yes by default
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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
Heng Li
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
Heng Li
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
Heng Li
306e4541f8
Released minimap2-2.3 (r531)
2017-10-22 23:13:35 -04:00
Heng Li
bd04372873
r524: reverted to bwa-mem end bonus
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and reduced the cost of clipping when filtering by identity
2017-10-20 16:57:31 -04:00
Heng Li
04cf4ebf5e
r518: increased the default -K to 500M
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This helps multi-thread performance for ultra-long reads.
2017-10-17 13:21:29 -04:00
Heng Li
e6f525edaf
r512: option to filter poorly aligned reads
2017-10-16 10:38:22 -04:00
Heng Li
858213d513
r511: fixed wrong primary sam record
2017-10-12 23:02:18 -04:00
Heng Li
7c555f9b7e
r508: use two I/O threads for mapping
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-x sr applies this option by default
2017-10-12 14:56:01 -04:00
Heng Li
7345621759
r499: end bonus working; DP region needs improve!
2017-10-11 00:14:25 -04:00
Heng Li
9396d9e11b
r452: typo in the last commit
2017-10-09 10:05:32 -04:00
Heng Li
198849a716
r491: an ambiguous base costs the same as gap ext
2017-10-09 09:59:42 -04:00
Heng Li
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
