b276772890
r1112: added --print-chains for debugging
2021-11-18 21:26:41 -05:00
39bdd45875
r1108: fixed missing inversions for #816 and #806
2021-10-04 16:34:30 -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
83a535f148
dev-r1084: fixed flag integer overflow
2021-07-19 11:52:18 -04:00
161ae7ff73
dev-r1079: per-read error rate
...
more tuning needed
2021-07-18 20:38:53 -04:00
2546999639
dev-r1076: log gap penalty
2021-07-17 18:23:59 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
379728726a
r1049: removed the long-join heuristics
2021-05-24 16:21:40 -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
da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -04:00
d2de282d21
remove second definition of kstring
2020-03-02 13:18:37 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
3c0d05d272
r962: abort given wrong RG line; resolves #541
2020-01-06 21:53:21 -05:00
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
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -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
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
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
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
f434653432
added peakrss(); not used for now
2018-02-17 20:40:31 -05:00
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
7ef5490884
r703: added --max-clip-ratio
...
still testing the option
2018-02-12 13:29:18 -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
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
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
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
e6f525edaf
r512: option to filter poorly aligned reads
2017-10-16 10:38:22 -04:00
c217eecdb7
r496: avoid DP extending into another chain
...
When deciding the region for DP, exclude regions in the adjacent chain
2017-10-10 17:25:12 -04:00
5ab99eb26e
more accurate SAM flag
2017-10-05 10:59:38 -04:00
7cc4f6f965
r469: first step towards PE SAM
2017-10-05 10:38:09 -04:00
7d50e646dd
r466: detect multi-part index more smartly
...
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
2017-10-04 17:32:58 -04:00
2a1e738a94
r461: randomize repetitive hits
2017-10-04 13:05:18 -04:00
9541052564
r447: paired-end mapping quality
...
not as good as I would hope...
2017-09-27 15:39:25 -04:00
7e0d70bfd3
r445: pair coordinate adjustment working
...
Next: mapq adjustment, which will be tricky...
2017-09-27 15:38:18 -04:00
55d1e4f638
r440: better chain filtering for PE reads
2017-09-26 11:03:36 -04:00
19d8eca3a1
moved array shrinking into chain_dp()
2017-09-20 14:58:57 -04:00
9943e5fdd0
backup
2017-09-20 14:35:46 -04:00
Heng Li
Jared Simpson