Heng Li
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fa99d28d34
|
r228: reduced unnecessary INV alignment
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2017-07-29 20:21:53 -04:00 |
|
Heng Li
|
d08b7a0c51
|
r227: use local alignment for INV alignment
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2017-07-29 17:40:53 -04:00 |
|
Heng Li
|
da3db3c095
|
r226: only try inv alignment for primary
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2017-07-29 14:09:35 -04:00 |
|
Heng Li
|
783ead6f47
|
r225: removed a debugging line
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2017-07-29 13:21:38 -04:00 |
|
Heng Li
|
19d6ec885e
|
r224: inversion alignment around Z-drop break
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2017-07-29 13:09:10 -04:00 |
|
Heng Li
|
120bebc290
|
ake
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2017-07-29 11:01:49 -04:00 |
|
Heng Li
|
5e3eecd6d4
|
r222: no effective changes
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2017-07-29 10:31:46 -04:00 |
|
Heng Li
|
ebbe9c1eb8
|
r219: fixed a bug caused by skipping tandem seeds
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2017-07-28 14:06:56 -04:00 |
|
Heng Li
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c672690564
|
r218: increase the frequency of SW slightly
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2017-07-28 13:30:42 -04:00 |
|
Heng Li
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f4fee60188
|
r217: ignore tandem seeds during alignment
This helps a tiny bit.
|
2017-07-28 12:26:56 -04:00 |
|
Heng Li
|
254280b8af
|
r216: a bit cleanup; identical output to r215
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2017-07-28 11:54:18 -04:00 |
|
Heng Li
|
2c79580649
|
r213: more careful solution to wrong seeds
a little better, but not good enough!
|
2017-07-27 13:19:11 -04:00 |
|
Heng Li
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b927838495
|
r212: better heuristic to fix wrong seeding
but not good enough. Will explore more.
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2017-07-27 11:24:51 -04:00 |
|
Heng Li
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371e20cc7c
|
r211: a better heurstic to reduce false seeds
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2017-07-26 23:56:38 -04:00 |
|
Heng Li
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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 |
|
Heng Li
|
38b2830e18
|
r161: filter bad seeds; changed default -g/-r
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2017-07-08 13:31:27 -04:00 |
|
Heng Li
|
cc554aee43
|
r159: use two-piece gap penalty
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2017-07-08 10:26:00 -04:00 |
|
Heng Li
|
2e4fd9f1d0
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r148: revamped regs handling after cigar
|
2017-07-03 10:44:26 -04:00 |
|
Heng Li
|
696ebce66e
|
backup; still buggy
|
2017-07-03 00:52:00 -04:00 |
|
Heng Li
|
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 |
|
Heng Li
|
d11049eb32
|
r120: use max-scoring seg to control output
much better now
|
2017-06-30 14:21:44 -04:00 |
|
Heng Li
|
5dcd8f8965
|
r117: fixed a bug in logic
|
2017-06-30 11:52:42 -04:00 |
|
Heng Li
|
91e1c4d6db
|
r116: fixed another bug caused by refactoring
|
2017-06-30 00:03:45 -04:00 |
|
Heng Li
|
e2b86d0332
|
r110: fixed a bug caused by refactoring
|
2017-06-29 21:12:31 -04:00 |
|
Heng Li
|
4cd456b9ba
|
r108: refactoring, move reg1 routines to hit.c
|
2017-06-29 19:44:11 -04:00 |
|
Heng Li
|
cc67f1b781
|
compute mapq; not working for z-split yet
|
2017-06-29 17:52:48 -04:00 |
|
Heng Li
|
337c2a21cd
|
r105: fixed a bug in repeated right ext when zdrop
|
2017-06-29 15:45:07 -04:00 |
|
Heng Li
|
b9075d39a8
|
r104: long gap patching
|
2017-06-29 14:54:54 -04:00 |
|
Heng Li
|
d274e1b743
|
backup
|
2017-06-29 12:58:52 -04:00 |
|
Heng Li
|
38070e8a05
|
r98: fixed segfault for certain scoring
due to unsigned comparisons between -1 and chromosome length
|
2017-06-28 22:18:51 -04:00 |
|
Heng Li
|
bcd9b1c621
|
r93: fixed various small issues
|
2017-06-28 10:35:21 -04:00 |
|
Heng Li
|
42283ef10c
|
r87: fixed a bug in ksw2
|
2017-06-27 13:29:48 -04:00 |
|
Heng Li
|
734028f92b
|
validate z-drop
|
2017-06-27 11:25:39 -04:00 |
|
Heng Li
|
c02ff4662c
|
r85: two-round z-drop
|
2017-06-27 10:36:24 -04:00 |
|
Heng Li
|
5b614ae828
|
r78: fixed a split bug
|
2017-06-26 14:45:23 -04:00 |
|
Heng Li
|
de54c9dac2
|
r77: fixed an index loading bug (offset not set)
|
2017-06-26 13:56:25 -04:00 |
|
Heng Li
|
24d7f7f8b1
|
disabled dynamic banding; buggy
|
2017-06-25 22:43:15 -04:00 |
|
Heng Li
|
39083be9ab
|
separated formating printing
for SAM in future; and for performance
|
2017-06-25 16:13:54 -04:00 |
|
Heng Li
|
7780ab792a
|
removed some comment lines
|
2017-06-25 11:53:35 -04:00 |
|
Heng Li
|
56364200c8
|
avoid contained hits due to split
|
2017-06-25 11:43:50 -04:00 |
|
Heng Li
|
f20d550a59
|
fixed the NM bug
due to reversed CIGAR
|
2017-06-25 11:24:39 -04:00 |
|
Heng Li
|
b261a4a74b
|
zdrop sort of works, but has issues
left and right extensions are different; NM is also wrong
|
2017-06-25 10:52:14 -04:00 |
|
Heng Li
|
72dfb0c99e
|
fixed a bug in ksw2
|
2017-06-25 10:22:13 -04:00 |
|
Heng Li
|
ef5dd318ca
|
implemented chain splitting; NOT tested!!!
|
2017-06-24 22:57:43 -04:00 |
|
Heng Li
|
aa5881e7bb
|
backup
|
2017-06-24 22:51:31 -04:00 |
|
Heng Li
|
d08b58d21f
|
minor
|
2017-06-24 19:33:59 -04:00 |
|
Heng Li
|
672782f03a
|
simplified hp_len a little
|
2017-06-24 19:27:58 -04:00 |
|
Heng Li
|
2d8fda9586
|
an alternative strategy to fix for HPC
it makes the result better, but still not quite right.
|
2017-06-24 09:26:24 -04:00 |
|
Heng Li
|
6088dc11ff
|
wrong SW score
|
2017-06-23 23:24:49 -04:00 |
|
Heng Li
|
2987be288c
|
output cigar
|
2017-06-23 22:53:47 -04:00 |