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
aefa2c0d86
added --chain-skip-scale
2021-10-01 16:58:03 -04:00
05a8a45d44
r1105: avoid long running time occasionally ( #771 )
...
Caused by highly repetitive minimizers on a query sequence. The solution is to
filter out these query minimizers.
2021-08-15 19:43:01 -04:00
7358a1ead1
Release minimap2-2.22 (r1101)
2021-08-07 11:30:31 -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
ef09ccf104
Release minimap2-2.19 (r1055)
2021-05-26 21:01:03 -04:00
34a41197d7
r1051: added two internal parameters
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rmq_rescue_size and rmq_rescue_ratio
2021-05-24 16:38:45 -04:00
379728726a
r1049: removed the long-join heuristics
2021-05-24 16:21:40 -04:00
4f91558160
r1048: rescue long gaps
2021-05-24 16:09:09 -04:00
8ec8866100
Merge branch 'master' into dev-rmq
2021-05-23 21:01:04 -04:00
9e7247cff9
sync python with recent changes
2021-05-23 21:00:15 -04:00
4422c0c6f9
Typo fix in Python README.
...
Thanks for sharing minimap2. Here's a little fix.
2021-05-14 15:38:12 -04:00
b6ff332de1
Release minimap2-2.18 (r1015)
2021-04-09 13:33:34 -04:00
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
9dceae59a0
r972: renamed --alt-diff to --alt-drop
2020-01-21 10:33:39 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
d2e14705e7
r968: allow large mini_batch; resolves #491
2020-01-18 12:24:44 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
238b6bb3ea
Fix memory leak in mappy.aligner.map.
2019-07-08 09:50:54 -04:00
03dc8d5d97
test if index is built for #413
2019-06-07 09:11:11 -04:00
7bc87b4175
Release minimap2-2.17 (r941)
2019-05-04 23:49:17 -04:00
97f67a2a0a
r937: enlarge mm_mapopt_t::flag to 64 bits
2019-04-30 22:30:32 -04:00
189555503a
potentially fix issue #372
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Needs someone to confirm
2019-04-30 21:49:51 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
6b391e3373
Release minimap2-2.16 (r922)
2019-02-28 15:49:24 -05:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
aaf3233818
added mappy.Aligner.seq_names to return seq names
...
Resolves #312
2019-01-29 12:53:20 -05:00
c404f49569
Release minimap2-2.15 (r905)
2019-01-10 12:34:45 -05:00
59f23f7579
Release minimap2-2.14 (r883)
2018-11-06 00:03:16 -05:00
8a2b1cd4c9
updated mappy for extra option max_sw_mat
2018-11-05 19:28:44 -05:00
5d5d392c02
Release minimap2-2.13 (r850)
2018-10-11 13:18:31 -04:00
791e89ce0f
PEP8 and other minor styles changes
2018-09-12 10:58:56 -04:00
9a567e4b37
allow mappy to change scoring
2018-08-06 09:52:13 -04:00
a1b7219b5d
explain added parameters
2018-08-05 21:32:05 -04:00
b0f39a1a61
r823: mappy to index a single sequence
2018-08-05 20:57:05 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
c92a6866f3
Release the GIL to allow native Python threading.
2018-07-05 08:00:27 -04:00
0517972d02
Release minimap2-2.11 (r797)
2018-06-21 00:04:08 -04:00
e9ca0c9dab
added __version__; resolved #165
...
Not sure if this is the right way. Apparently working.
2018-06-19 15:40:26 -04:00
1bde2cf076
Allow setting max_frag_len on a per alignment level
2018-06-19 14:39:30 -04:00
31fc0f218a
Allow setting max_frag_len parameter in Aligner class
2018-06-19 14:39:30 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
ee4cd089f7
r763: fine control long join flank len ( #128 )
2018-03-29 14:16:58 -04:00
7938ed4893
fixed two mappy warnings
2018-03-26 15:12:54 -04:00
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
96b132c97d
fixed a bug/typo in Aligner.seq() ( #126 )
2018-03-08 19:12:12 -05:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
Heng Li
John Marshall
Don Kirkby
Marcus Stoiber
Chris Rands
Hyeshik Chang
mvdbeek