dfc78b39d3
refactor the old sorting
2018-01-26 09:37:48 -05:00
7b57c9a619
heap sort working on MT
2018-01-26 09:21:45 -05:00
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
dd18307e66
code backup
2018-01-25 21:52:49 -05:00
543fa12e68
r659: for C++ compatibility
2018-01-19 10:40:18 -05:00
af1a871270
r658: gives a warning if -N0 is used
2018-01-19 08:33:20 -05:00
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
0454e6be91
explain -M in the manpage
2018-01-18 11:47:11 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -05:00
eecc06086f
Released minimap2-2.7 (r654)
2018-01-09 13:16:00 -05:00
dfea113f28
r653: the last change may write "N" wrongly
2018-01-08 11:33:53 -05:00
1842d7f5b5
allow to exclude regions
2018-01-07 22:35:56 -05:00
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
248b43cc47
work with targets in BED12
2018-01-07 19:39:25 -05:00
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
7b5a601d48
support paired-end reads
...
this gives unnecessary warnings, which will be fixed later.
2018-01-07 13:53:26 -05:00
405d531100
don't test python v3.3
2018-01-05 22:17:00 -05:00
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
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
...
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
...
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
...
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
...
* 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
Heng Li
Hasindu Gamaarachchi