d431dc0181
r917: added --max-chain-iter to avoid worst case
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Resolves #324
2019-02-27 14:41:01 -05:00
aaf3233818
added mappy.Aligner.seq_names to return seq names
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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
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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
29ed675ee5
bugfix: in-place revcomp() not working
2018-02-20 11:05:54 -05:00
7dc7097208
added reverse complement
2018-02-20 09:41:25 -05:00
090361c25b
fixed a typo in mappy ( #117 )
2018-02-16 21:10:57 -05:00
1372977a37
r708: implemented double Z-drop thresholds ( #112 )
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When aligning long reads, we would prefer to align through low-quality
regions. This requires a large Z-drop threshold. However, to find small
inversions, we need to use a small Z-drop. This commit address this
conflict with two Z-drop thresholds. When Z-drop exceeds the smaller
threshold, we perform a local alignment to check if there is a potential
inversion. If there is one, we break the alignment; otherwise we break
the alignment only if Z-drop excess the larger threshold.
This commit also fixes a bug that reported wrong coordinates when the
inversion is on the forward strand (#112 ).
2018-02-15 10:50:49 -05:00
7ef5490884
r703: added --max-clip-ratio
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still testing the option
2018-02-12 13:29:18 -05:00
29b4a1786c
r685: tune end seed filter again
2018-02-05 11:48:22 -05:00
dbf284b2d9
r684: separate end score from min_chain_score
2018-02-05 11:40:38 -05:00
46d6349af4
r670: added PE support to mappy
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and minor code cleanup
2018-01-31 11:33:08 -05:00
eb819c29e8
Release minimap2-2.6 (r623)
2017-12-12 11:09:59 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
4f77b0c1ed
Fix typo in strand property
2017-11-11 01:18:44 +00:00
29a26e3eea
Bug fix with byte strings in Python3
2017-11-09 13:57:15 +00:00
21a46ba652
Release minimap2-2.4 (r555)
2017-11-06 12:54:02 -05:00
b24c9c90c7
updated mappy and example.c
2017-10-16 11:15:07 -04:00
de2fcc1bf3
updated the mappy
2017-10-05 17:10:07 -04:00
ea5a0cd17d
Release minimap2-2.2 (r409)
2017-09-17 20:08:47 -04:00
cf93e5c0a1
more functional minimap2.py; added categories
2017-09-17 17:06:39 -04:00
0b660c70e2
syntax error
2017-09-17 16:02:06 -04:00
5715c423ff
exposed timer and verbose-level to mappy
2017-09-17 15:21:36 -04:00
c8a019fae8
exposed fasta/q reader to mappy
2017-09-17 14:41:59 -04:00
3edf2a9130
renamed mm2-lite.py to minimap2.py
2017-09-17 09:41:37 -04:00
d5012a1b17
this is embarrassing: rename again to mappy
2017-09-17 00:05:30 -04:00
ef46a8aed4
remaining minimap2=>mmappy in doc
2017-09-16 23:49:02 -04:00
28fd3d63fd
renamed module name from minimap2 to mmappy
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minimap2 clashed with minimap2 from conda
2017-09-16 23:29:41 -04:00
8cdaae0935
fixed a few typos
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eh... a missing fix
2017-09-16 22:53:24 -04:00
1d90742b35
fixed hyperlink
2017-09-16 22:46:30 -04:00
5103cea7d3
load python README.rst into setup.py
2017-09-16 22:43:52 -04:00
7da9a08a6f
reformat
2017-09-16 22:36:19 -04:00
Heng Li
Chris Rands
Hyeshik Chang
mvdbeek
cwright
martinghunt