34a41197d7
r1051: added two internal parameters
...
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
9e7247cff9
sync python with recent changes
2021-05-23 21:00:15 -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
97f67a2a0a
r937: enlarge mm_mapopt_t::flag to 64 bits
2019-04-30 22:30:32 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
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Resolves #324
2019-02-27 14:41:01 -05:00
8a2b1cd4c9
updated mappy for extra option max_sw_mat
2018-11-05 19:28:44 -05:00
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
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
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
1372977a37
r708: implemented double Z-drop thresholds ( #112 )
...
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
...
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
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
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
d5012a1b17
this is embarrassing: rename again to mappy
2017-09-17 00:05:30 -04:00
Heng Li