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
8a1d52bcbe
r1094: for --split-prefix update max_dp at the end
2021-08-06 21:40:43 -04:00
5180b70ff3
r1090: log wall-clock time for each read
2021-08-04 17:45:09 -04:00
2392e54fe2
r1089: fixed an unusual memory leak ( #749 )
...
This is more apparent when there are many candidate chains. Although only a
small numbers of them are extended, they are still occupying memory. A
realloc() solves this problem. This is a long existiing issue.
2021-08-04 17:07:00 -04:00
7e33fde82b
dev-r1087: added --cap-kalloc
2021-07-19 21:20:04 -04:00
5f449c5cae
fixed potential integer overflows
2021-07-16 17:20:05 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
15471bd629
Release minimap2-2.20 (r1061)
2021-05-27 15:26:04 -04:00
ca19463268
r1060: safer ways to use -rNUM1,NUM2
2021-05-27 10:55:13 -04:00
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
ec3bc6efd7
r1047: make gap penalty proportional to k-mer
...
closer to the older minimap2
2021-05-24 13:18:17 -04:00
bbb4f97e52
support RMQ
2021-05-03 09:27:04 -04:00
b7f4d8a0f4
removed the old minimap2 chaining
2021-05-02 18:55:37 -04:00
e81927e7a1
prepare to backport unimap/minigraph chaining
2021-05-02 18:25:49 -04:00
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
cdbd96be0c
a bit refactoring for future changes
2021-04-30 11:24:53 -04:00
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
9c0e2c67f8
r986: don't estimate dv with --qstrand
2020-04-21 13:21:03 -04:00
da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -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
20c104ce8d
Report errno on file opening failures and I/O errors
...
Add the underlying operating system error (usually "No such file" or
"Out of space" respectively, but highly informative when it is not)
to these error messages.
2019-07-17 09:04:02 -04:00
c2aec88b84
r938: added --sam-hit-only; resolved #377
2019-04-30 22:40:36 -04:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
1739a260fb
r913: output tag "rl", length of unseedable regs
2019-02-05 14:19:17 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
b32296e18f
r821: fixed memory when -y is used
2018-07-31 15:14:37 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
a655cbef86
print SAM header; remove tmp files
2018-07-15 11:03:18 -04:00
4b707aac92
working with toy examples
2018-07-15 10:55:00 -04:00
3545e35a42
pairing in the split-idx mode
2018-07-14 23:43:34 -04:00
e5277dbf5c
code backup
2018-07-14 22:52:36 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
3573784b4d
r782: no mask a chain having long ref ovlp ( #155 )
2018-05-30 13:53:45 -04:00
872f300955
r781: fixed the buggy heapmerge ( resolves #166 )
2018-05-30 11:55:14 -04:00
08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
da6947cfa3
r671: cleanup command line options
2018-01-31 13:59:52 -05:00
46d6349af4
r670: added PE support to mappy
...
and minor code cleanup
2018-01-31 11:33:08 -05:00
Heng Li
John Marshall