Heng Li
6205fa6f21
document --heap-sort
2018-01-26 15:15:40 -05:00
Heng Li
d676a5314b
r664: use --heat-sort for sr by default
2018-01-26 12:25:42 -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
543fa12e68
r659: for C++ compatibility
2018-01-19 10:40:18 -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 )
...
Well, in principle, every option should be checked. Will do when someone raise
issues...
2018-01-19 01:03:38 -05:00
Heng Li
0454e6be91
explain -M in the manpage
2018-01-18 11:47:11 -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
eecc06086f
Released minimap2-2.7 (r654)
2018-01-09 13:16:00 -05:00
Heng Li
dfea113f28
r653: the last change may write "N" wrongly
2018-01-08 11:33:53 -05:00
Heng Li
1842d7f5b5
allow to exclude regions
2018-01-07 22:35:56 -05:00
Heng Li
f5cfd439ee
r651: incorrectly treat introns as deletions
...
This happened when the last operation during backtracking is an intron.
2018-01-07 19:42:50 -05:00
Heng Li
248b43cc47
work with targets in BED12
2018-01-07 19:39:25 -05:00
Heng Li
bf72969ab1
added a bed counter
...
I know there are tools for this purpose, but they don't quite meet my exact
need.
2018-01-07 15:19:18 -05:00
Heng Li
7b5a601d48
support paired-end reads
...
this gives unnecessary warnings, which will be fixed later.
2018-01-07 13:53:26 -05:00
Heng Li
405d531100
don't test python v3.3
2018-01-05 22:17:00 -05:00
Heng Li
e9607fcd9b
allow to convert read names
...
ONT read names are just too long and too hard to compress
2018-01-05 22:05:15 -05:00
Heng Li
a465a920ec
bug in block starts; added color and short-name
2018-01-05 21:45:56 -05:00
Heng Li
b20839be77
more robust ID conversion
2018-01-05 17:55:24 -05:00
Heng Li
209beb9955
convert EnsEMBL to UCSC name (optional)
2018-01-05 17:41:18 -05:00
Heng Li
cfe87f50c1
convert GTF/GFF3 to BED12
2018-01-05 17:10:43 -05:00
Heng Li
680b971bb0
deleted duplicated entries
2018-01-01 19:52:21 -05:00
Heng Li
6b0d3c1fa8
added PHONY and comments to makefile
2017-12-30 20:54:11 -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
...
I haven't figured out the exact bounds...
2017-12-30 07:50:40 -05:00
Heng Li
f159e1c2d3
new section on HPC k-mers
2017-12-24 19:11:23 -05:00
Heng Li
3a375d3436
renamed paf2ovlp to ov-eval
2017-12-24 18:04:00 -05:00
Heng Li
626f10e0d0
evaluate sensitivity in the same script
2017-12-24 17:55:42 -05:00
Heng Li
b997578078
find reads overlaps based on reference alignment
2017-12-24 17:20:27 -05:00
Heng Li
ce8a48d715
fixed two minor typos in references
2017-12-24 13:14:47 -05:00
Heng Li
99879e9e75
a new section on estimating sequence divergence
2017-12-24 12:57:38 -05:00
Heng Li
c969d1a1ce
updated direct RNA-seq results; cite syndip
...
and a few minor changes
2017-12-24 11:06:17 -05:00
Heng Li
fcac296c4a
clarify ARM-NEON support in README
2017-12-18 23:01:44 -05:00
Heng Li
e420b17496
r629: API to construct index from strings
2017-12-18 22:29:46 -05:00
Heng Li
23a846c594
Merge pull request #81 from hasindu2008/master
...
minimap2 on ARM processors
2017-12-16 09:40:41 -05:00
Heng Li
ab345e600b
r626: function to check incorrect scoring system
2017-12-13 12:23:43 -05:00
Heng Li
d003a00d71
r625: HPC sketch still has one minor issue
2017-12-13 09:40:42 -05:00
Heng Li
ae85dcde76
added esterr.o dependencies
2017-12-13 09:01:48 -05:00
Heng Li
eb819c29e8
Release minimap2-2.6 (r623)
2017-12-12 11:09:59 -05:00
Heng Li
fb630de40a
r622: fixed bug in sdust due to recent refactor
2017-12-11 15:32:28 -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
...
* 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
0e42628ef6
r611: document --idx-no-seq; better inv aln
2017-12-08 13:16:18 -05:00
Heng Li
98a999fe44
r611: added pseudocount when est divergence
2017-12-08 12:57:57 -05:00
Heng Li
fec7bd713f
r610: warning if db sequence is 0-lengthed ( #69 )
2017-12-07 21:05:39 -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
...
Currently using the simplest method. There may be a more accurate estimate.
2017-12-06 16:14:39 -05:00
Heng Li
68c63f2d68
r606: fixed a sketch bug for long 256bp k-mer
...
sketch() writes {-1,-1} to the output array.
2017-12-06 16:13:29 -05:00
Heng Li
76206f574f
support both SAM and PAF as input
2017-12-02 21:57:19 -05:00
Heng Li
e575f884e1
convert spliced PAF to BED
2017-12-02 21:23:41 -05:00
Heng Li
571161d5a2
changed badges
2017-12-01 16:16:27 -05:00
Heng Li
07d41efc2b
explain secondary/supplementary aln for RNA-seq
2017-11-30 23:02:20 -05:00
Heng Li
984f7846c0
r601: bugfix - a similar issue to r600
...
This bug unsets the alignment score of suboptimal alignments.
2017-11-30 11:51:34 -05:00
Heng Li
af1d6afba9
r600: bugfix - missing secondary alignments ( #71 )
...
This should very rarely happen to typical data, but has a higher chance in
artifactual data.
2017-11-30 11:34:10 -05:00
Heng Li
cbdb6c069f
when there are incorrect anno, warn but not abort
2017-11-24 12:48:49 -05:00
Heng Li
35b6d9f7d5
direct manpage to HTML
2017-11-24 11:05:20 -05:00
Heng Li
39a9666246
convert PAF to LAST's cigar output
...
also added the support of BLAST-like output for "--cs=short".
2017-11-18 20:30:44 -05:00
Heng Li
662d05dc02
fixed incorrect var coordinate
2017-11-12 20:25:33 -05:00
Heng Li
379457c18b
use mapq threshold
2017-11-12 19:01:34 -05:00
Heng Li
03169d590b
print cov-1 regions (not BED output any more)
2017-11-12 18:45:49 -05:00
Heng Li
8c8d446820
find regions covered by one contig
2017-11-12 18:41:01 -05:00
Heng Li
0ddb064f17
dnadiff-like script; improvement coming
2017-11-12 15:07:29 -05:00
Heng Li
131cfc6938
r574: build index without sequences
2017-11-11 21:38:38 -05:00
Heng Li
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
Heng Li
3b518271ee
Release minimap2-2.5 (r572)
2017-11-11 11:29:28 -05:00
Heng Li
481d8239e9
Merge pull request #57 from cjw85/strand_typo
...
Fix typo in strand property
2017-11-10 20:36:19 -05:00
Heng Li
d7a31e40e6
r569: last commit is buggy
2017-11-09 23:20:41 -05:00
Heng Li
dd18cd75de
r568: revert - don't take max(dp_max, dp_score)
2017-11-09 23:12:48 -05:00
Heng Li
99a2709913
r567: minor change to #56
2017-11-09 19:17:45 -05:00
Heng Li
032068a747
Merge pull request #56 from mvdbeek/softclipping
...
Implement -Y for soft clipping of supp. alignments
2017-11-09 19:12:47 -05:00
Heng Li
422b43374e
Merge pull request #55 from martinghunt/fix_python3_strings
...
Bug fix with byte strings in Python3
2017-11-09 09:37:41 -05:00
Heng Li
a7b38f6900
r562: fixed a severe bug: wrong query start
2017-11-08 22:31:05 -05:00
Heng Li
e896c9ec05
r559: prefer a chain involving more segments
2017-11-08 13:22:16 -05:00
Heng Li
98ba8928c6
r558: dp_max no less than dp_score
2017-11-08 10:06:10 -05:00
Heng Li
bcf8462d20
Merge pull request #52 from cvdelannoy/patch-1
...
Update README.md
2017-11-08 07:50:31 -05:00
Heng Li
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
Heng Li
65deedfa96
r556: bugfix - underestimate mapq for split aln
2017-11-07 22:37:12 -05:00
Heng Li
21a46ba652
Release minimap2-2.4 (r555)
2017-11-06 12:54:02 -05:00
Heng Li
1617b87ee1
this will become version 3 at arXiv
2017-11-06 10:57:12 -05:00
Heng Li
2191ac58ad
two discussion paragraphs; need one more
2017-11-05 12:27:52 -05:00
Heng Li
fa5a645ca5
r552: fixed a tiny typo on struct packing
...
The old packing wastes memory, thought very small.
2017-11-05 08:27:26 -05:00
Heng Li
c2b09356b8
moved conclusion to result; need new discussion
2017-11-04 22:19:46 -04:00
Heng Li
a3f0aa1d5b
r550: fixed -L issues with secondary and supp aln
2017-11-04 12:13:38 -04:00
Heng Li
52ffbc9e0c
added bowtie2 and snap versions
2017-11-02 15:51:23 -04:00
Heng Li
a9790c0f1d
added two bowtie2 numbers for comparison
2017-11-02 15:44:48 -04:00
Heng Li
d0ac78ac08
updated the tech note
2017-11-02 15:37:24 -04:00
Heng Li
22290db3e4
r546: minor mapQ tuning
2017-11-01 13:20:39 -04:00
Heng Li
cd24dc8834
r545: removed option -i, not working well
2017-10-31 22:23:27 -04:00
Heng Li
b8e758df0f
r544: increased PE mapQ
2017-10-31 16:55:02 -04:00
Heng Li
311fa90030
r543: applied some sr mapq changes to long reads
2017-10-31 15:24:05 -04:00
Heng Li
fb8a1b5536
r542: tuning mapQ calculation
2017-10-31 14:25:09 -04:00
Heng Li
7f11f4c4d4
Instructions on different long RNA-seq techs
2017-10-29 13:58:25 -04:00
Heng Li
285eb0da05
r540: removed a buggy debugging line
2017-10-29 00:02:41 -04:00
Heng Li
192217a10c
r539: use --splice-flank=yes by default
...
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
f22a94e868
r538: fixed a long existing bug in HPC k-mer ( #47 )
...
This bug may lead to a wrong minimizer when a HPC k-mer is longer than 256bp.
When there is a seed match involving this wrong HPC k-mer, the correct seed
sequences do not match in fact. This violates the assumption in align.c and
subsequently causes a segfault, which is what #47 has caught. This bug lurked
in the earliest piece of code and affected all released minimap2 versions so
far. It is extremely rare and does not affect the prebuilt GRCh37/38 indices.
2017-10-28 19:21:10 -04:00
Heng Li