e9607fcd9b
allow to convert read names
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ONT read names are just too long and too hard to compress
2018-01-05 22:05:15 -05:00
a465a920ec
bug in block starts; added color and short-name
2018-01-05 21:45:56 -05:00
b20839be77
more robust ID conversion
2018-01-05 17:55:24 -05:00
209beb9955
convert EnsEMBL to UCSC name (optional)
2018-01-05 17:41:18 -05:00
cfe87f50c1
convert GTF/GFF3 to BED12
2018-01-05 17:10:43 -05:00
680b971bb0
deleted duplicated entries
2018-01-01 19:52:21 -05:00
6b0d3c1fa8
added PHONY and comments to makefile
2017-12-30 20:54:11 -05:00
dc9e3dcf4a
r639: changed -O/-E validation
2017-12-30 20:39:29 -05:00
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
f159e1c2d3
new section on HPC k-mers
2017-12-24 19:11:23 -05:00
3a375d3436
renamed paf2ovlp to ov-eval
2017-12-24 18:04:00 -05:00
626f10e0d0
evaluate sensitivity in the same script
2017-12-24 17:55:42 -05:00
b997578078
find reads overlaps based on reference alignment
2017-12-24 17:20:27 -05:00
ce8a48d715
fixed two minor typos in references
2017-12-24 13:14:47 -05:00
99879e9e75
a new section on estimating sequence divergence
2017-12-24 12:57:38 -05:00
c969d1a1ce
updated direct RNA-seq results; cite syndip
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and a few minor changes
2017-12-24 11:06:17 -05:00
fcac296c4a
clarify ARM-NEON support in README
2017-12-18 23:01:44 -05:00
e420b17496
r629: API to construct index from strings
2017-12-18 22:29:46 -05:00
23a846c594
Merge pull request #81 from hasindu2008/master
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minimap2 on ARM processors
2017-12-16 09:40:41 -05:00
8995e2e078
added support for arm neon
2017-12-15 17:42:19 +11:00
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
ae85dcde76
added esterr.o dependencies
2017-12-13 09:01:48 -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
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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
Heng Li
Hasindu Gamaarachchi