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
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
12a5a5fa3c
r669: improved self chain extension ( #10 )
...
This has not fully resolved #10 , only alleviated the issue.
2018-01-30 20:05:02 -05:00
dfc78b39d3
refactor the old sorting
2018-01-26 09:37:48 -05:00
7b57c9a619
heap sort working on MT
2018-01-26 09:21:45 -05:00
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
dd18307e66
code backup
2018-01-25 21:52:49 -05:00
af1a871270
r658: gives a warning if -N0 is used
2018-01-19 08:33:20 -05:00
2b71181a37
r657: check -p ( #96 )
...
Well, in principle, every option should be checked. Will do when someone raise
issues...
2018-01-19 01:03:38 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -05:00
dc9e3dcf4a
r639: changed -O/-E validation
2017-12-30 20:39:29 -05:00
cc75c12905
r638: disabled scoring checking
...
I haven't figured out the exact bounds...
2017-12-30 07:50:40 -05:00
ab345e600b
r626: function to check incorrect scoring system
2017-12-13 12:23:43 -05:00
43960a8ca7
r621: --print-qname also shows kalloc status
2017-12-11 12:30:08 -05:00
f6608fe99c
r620: revamped thread-local memory management
...
* Don't preallocate sdust_buf or minizer list. kalloc should be fast enough -
benchmarks needed to confirm.
* Fixed a memory leak caused by divergence estimate (post v2.5)
* Reset the kalloc buffer after mapping a long query. This reduces peak memory
when large chunks of memory are allocated, at the cost of performance, though.
2017-12-11 12:11:10 -05:00
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
824712a4ee
r617: removed some unused code
2017-12-10 17:54:50 -05:00
98a999fe44
r611: added pseudocount when est divergence
2017-12-08 12:57:57 -05:00
2f693e8ca4
r609: bugfix - SDUST masking not working
2017-12-07 11:45:38 -05:00
704ff9f4c6
r607: estimate sequence divergence
...
Currently using the simplest method. There may be a more accurate estimate.
2017-12-06 16:14:39 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
cd24dc8834
r545: removed option -i, not working well
2017-10-31 22:23:27 -04:00
fb8a1b5536
r542: tuning mapQ calculation
2017-10-31 14:25:09 -04:00
Heng Li
John Marshall