eccdb3a1ca
r315: added getopt from musl
2017-09-01 20:20:34 +08:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
993a2bb521
r301: separate introns from deletions
...
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
2017-08-18 15:31:15 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
b5f5929bf9
r296: expose splicing related options to CLI
2017-08-13 21:37:51 -04:00
28f86688ab
r295: gap closure from the middle of non-HPC k
...
This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
2017-08-12 23:48:43 -04:00
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
0f4c823b0c
r286: ignore introns when computing max seg score
2017-08-12 10:58:16 -04:00
163fa36ee6
r281: don't open long gaps on query
2017-08-10 15:04:59 -04:00
1a7d782131
r273: cdna mapping mode for testing
...
Differences from the typical mapping mode:
* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
2017-08-08 11:31:49 -04:00
5934d68772
r229: a new way to prevent out-of-band backtrack
2017-07-29 23:52:30 -04:00
fa99d28d34
r228: reduced unnecessary INV alignment
2017-07-29 20:21:53 -04:00
d08b7a0c51
r227: use local alignment for INV alignment
2017-07-29 17:40:53 -04:00
da3db3c095
r226: only try inv alignment for primary
2017-07-29 14:09:35 -04:00
783ead6f47
r225: removed a debugging line
2017-07-29 13:21:38 -04:00
19d6ec885e
r224: inversion alignment around Z-drop break
2017-07-29 13:09:10 -04:00
120bebc290
ake
2017-07-29 11:01:49 -04:00
5e3eecd6d4
r222: no effective changes
2017-07-29 10:31:46 -04:00
ebbe9c1eb8
r219: fixed a bug caused by skipping tandem seeds
2017-07-28 14:06:56 -04:00
c672690564
r218: increase the frequency of SW slightly
2017-07-28 13:30:42 -04:00
f4fee60188
r217: ignore tandem seeds during alignment
...
This helps a tiny bit.
2017-07-28 12:26:56 -04:00
254280b8af
r216: a bit cleanup; identical output to r215
2017-07-28 11:54:18 -04:00
2c79580649
r213: more careful solution to wrong seeds
...
a little better, but not good enough!
2017-07-27 13:19:11 -04:00
b927838495
r212: better heuristic to fix wrong seeding
...
but not good enough. Will explore more.
2017-07-27 11:24:51 -04:00
371e20cc7c
r211: a better heurstic to reduce false seeds
2017-07-26 23:56:38 -04:00
f2ef48878a
r202: trim bad chain ends before extension
...
This fixes a few more FP long INDELs towards the end of alignments.
2017-07-25 19:53:19 -04:00
38b2830e18
r161: filter bad seeds; changed default -g/-r
2017-07-08 13:31:27 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
696ebce66e
backup; still buggy
2017-07-03 00:52:00 -04:00
426c2975f6
r126: filter by fraction of seed coverage
...
otherwise we may get too many poor overlap mappings.
2017-06-30 22:15:45 -04:00
d11049eb32
r120: use max-scoring seg to control output
...
much better now
2017-06-30 14:21:44 -04:00
5dcd8f8965
r117: fixed a bug in logic
2017-06-30 11:52:42 -04:00
91e1c4d6db
r116: fixed another bug caused by refactoring
2017-06-30 00:03:45 -04:00
e2b86d0332
r110: fixed a bug caused by refactoring
2017-06-29 21:12:31 -04:00
4cd456b9ba
r108: refactoring, move reg1 routines to hit.c
2017-06-29 19:44:11 -04:00
cc67f1b781
compute mapq; not working for z-split yet
2017-06-29 17:52:48 -04:00
337c2a21cd
r105: fixed a bug in repeated right ext when zdrop
2017-06-29 15:45:07 -04:00
b9075d39a8
r104: long gap patching
2017-06-29 14:54:54 -04:00
d274e1b743
backup
2017-06-29 12:58:52 -04:00
38070e8a05
r98: fixed segfault for certain scoring
...
due to unsigned comparisons between -1 and chromosome length
2017-06-28 22:18:51 -04:00
bcd9b1c621
r93: fixed various small issues
2017-06-28 10:35:21 -04:00
42283ef10c
r87: fixed a bug in ksw2
2017-06-27 13:29:48 -04:00
734028f92b
validate z-drop
2017-06-27 11:25:39 -04:00
c02ff4662c
r85: two-round z-drop
2017-06-27 10:36:24 -04:00
5b614ae828
r78: fixed a split bug
2017-06-26 14:45:23 -04:00
de54c9dac2
r77: fixed an index loading bug (offset not set)
2017-06-26 13:56:25 -04:00
24d7f7f8b1
disabled dynamic banding; buggy
2017-06-25 22:43:15 -04:00
Heng Li