16b8d50199
removed debugging code
2023-01-06 11:16:09 -05:00
822ccd1733
r1152: evaluate base Sn and Sp
2022-11-01 21:58:45 -04:00
f67849c9af
r1151: added exoneval
2022-11-01 21:10:35 -04:00
2a319c89aa
support ##PAF lines in GFF3
2022-10-07 19:34:25 -04:00
5aa4355ca8
extract junctions from GFF
2022-09-21 12:57:40 -04:00
6ed7263670
junceval for plain junction BED as input
2022-09-10 23:18:08 -04:00
315795eefd
skip unmapped lines
2022-09-10 08:48:57 -04:00
fc6869a9e8
r1141: junceval to support miniprot output
2022-09-09 16:28:23 -04:00
6252e5e367
sync with tag changes in miniprot
2022-09-09 14:48:17 -04:00
843729df1e
output CDS and stop_codon
2022-09-09 12:09:38 -04:00
195c98fa46
output dist from end instead
2022-09-08 23:35:48 -04:00
a2e6659d9b
output more info
2022-09-08 23:18:13 -04:00
e450f161bb
added paf2gff
2022-09-08 22:33:21 -04:00
15cade0f06
added longcs2fa
2022-07-18 22:24:48 -04:00
50a26a60a6
option to keep Ensembl_canonical only
2022-05-14 11:18:06 -04:00
31de4fd1bc
r1132: document misjoin output
...
Also additional check of centromeric breakpoints
2022-05-11 21:39:29 -04:00
fe35e679e9
Release minimap2-2.24 (r1122)
2021-12-26 15:14:54 -05:00
d0cff3eb36
Release minimap2-2.23 (r1111)
2021-11-18 17:11:48 -05:00
7ee62dae1d
updated manuscript
2021-10-01 11:42:36 -04:00
7358a1ead1
Release minimap2-2.22 (r1101)
2021-08-07 11:30:31 -04:00
a05edfa5ec
a different ending sentence
2021-08-07 10:38:48 -04:00
f7271a7c24
expose mapQ threshold to command line of pafcmp
2021-08-06 19:41:46 -04:00
9d049f0562
added pafcmp
2021-08-05 12:41:21 -04:00
629c11728e
output the number of mismatches
2021-08-04 17:05:06 -04:00
c4fe52fb07
reduced the default -l and -b
2021-07-19 17:25:11 -04:00
ead1cfbaca
output for binning
2021-07-19 14:56:33 -04:00
f3af29a8aa
don't add a new command
2021-07-19 10:57:48 -04:00
cf7eaef367
refactor and prepare for a new command
2021-07-19 00:36:17 -04:00
2411887d8e
rename
2021-07-19 00:30:16 -04:00
15118dd521
output #mismatches/#dels/#ins in view
2021-07-18 15:13:40 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
581f2d7123
Release minimap2-2.21 (r1071)
2021-07-06 13:18:55 -04:00
177eef259d
Use the full MIDNSHP=X string whenever printing CIGAR strings
...
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.
It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
2021-07-02 13:03:03 -04:00
15471bd629
Release minimap2-2.20 (r1061)
2021-05-27 15:26:04 -04:00
9febf532c1
Release minimap2-2.19 (r1057)
2021-05-26 21:23:42 -04:00
ef09ccf104
Release minimap2-2.19 (r1055)
2021-05-26 21:01:03 -04:00
f31705bb4a
r1053: made junceval work with PAF
2021-05-26 11:54:46 -04:00
cd9ccfa069
r1022: check INDEL lengths in simple cases
2021-04-11 22:07:00 -04:00
86b716448c
larger window size for longer INDELs
2021-04-11 16:08:29 -04:00
9ab95be1bb
update END when it is not there
2021-04-11 12:59:21 -04:00
b51e859945
make sure ins/del match
2021-04-11 11:47:14 -04:00
a9037dc16c
r1018: scripts for SV evaluation
2021-04-11 01:08:17 -04:00
b6ff332de1
Release minimap2-2.18 (r1015)
2021-04-09 13:33:34 -04:00
1b0bb7b0ba
require overlap ratio when considering centromere
2021-03-11 19:11:44 -05:00
ecbc399fa2
improved sveval
2021-03-06 19:44:13 -05:00
4dfd495cc2
added sveval
2021-02-15 14:49:36 -05:00
194b457e79
option to print errors only
2021-02-07 12:58:03 -05:00
75c8933511
evaluate large-scale misjoins
2021-02-07 12:34:13 -05:00
1025993469
print number of errors on each read
2021-01-29 14:08:21 -05:00
a3253d1a6b
added a command for simple VCF statistics
2021-01-14 12:24:38 -05:00
Heng Li
John Marshall