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
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
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
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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
76206f574f
support both SAM and PAF as input
2017-12-02 21:57:19 -05:00
e575f884e1
convert spliced PAF to BED
2017-12-02 21:23:41 -05:00
571161d5a2
changed badges
2017-12-01 16:16:27 -05:00
07d41efc2b
explain secondary/supplementary aln for RNA-seq
2017-11-30 23:02:20 -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 )
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This should very rarely happen to typical data, but has a higher chance in
artifactual data.
2017-11-30 11:34:10 -05:00
cbdb6c069f
when there are incorrect anno, warn but not abort
2017-11-24 12:48:49 -05:00
35b6d9f7d5
direct manpage to HTML
2017-11-24 11:05:20 -05:00
39a9666246
convert PAF to LAST's cigar output
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also added the support of BLAST-like output for "--cs=short".
2017-11-18 20:30:44 -05:00
662d05dc02
fixed incorrect var coordinate
2017-11-12 20:25:33 -05:00
379457c18b
use mapq threshold
2017-11-12 19:01:34 -05:00
03169d590b
print cov-1 regions (not BED output any more)
2017-11-12 18:45:49 -05:00
8c8d446820
find regions covered by one contig
2017-11-12 18:41:01 -05:00
0ddb064f17
dnadiff-like script; improvement coming
2017-11-12 15:07:29 -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
481d8239e9
Merge pull request #57 from cjw85/strand_typo
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Fix typo in strand property
2017-11-10 20:36:19 -05:00
4f77b0c1ed
Fix typo in strand property
2017-11-11 01:18:44 +00:00
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
032068a747
Merge pull request #56 from mvdbeek/softclipping
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Implement -Y for soft clipping of supp. alignments
2017-11-09 19:12:47 -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
422b43374e
Merge pull request #55 from martinghunt/fix_python3_strings
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Bug fix with byte strings in Python3
2017-11-09 09:37:41 -05:00
29a26e3eea
Bug fix with byte strings in Python3
2017-11-09 13:57:15 +00:00
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
bcf8462d20
Merge pull request #52 from cvdelannoy/patch-1
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Update README.md
2017-11-08 07:50:31 -05:00
c047c852ce
Update README.md
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25: changed -x ava-one to -x ava-ont
2017-11-08 13:07:01 +01:00
b24d68ae9f
r557: fixed another mapq underestimate
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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
1617b87ee1
this will become version 3 at arXiv
2017-11-06 10:57:12 -05:00
2191ac58ad
two discussion paragraphs; need one more
2017-11-05 12:27:52 -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
c2b09356b8
moved conclusion to result; need new discussion
2017-11-04 22:19:46 -04:00
a3f0aa1d5b
r550: fixed -L issues with secondary and supp aln
2017-11-04 12:13:38 -04:00
52ffbc9e0c
added bowtie2 and snap versions
2017-11-02 15:51:23 -04:00
a9790c0f1d
added two bowtie2 numbers for comparison
2017-11-02 15:44:48 -04:00
Heng Li
cwright
mvdbeek
martinghunt
Carlos de Lannoy