Heng Li
|
9fbf7e41e1
|
r99: report progress
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2017-06-28 23:56:33 -04:00 |
|
Heng Li
|
cf703655cb
|
optional sse4
|
2017-06-28 22:21:52 -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
|
5e202afb5f
|
fixed invalid backtracking, a temporary solution
|
2017-06-28 18:17:57 -04:00 |
|
Heng Li
|
a25866c25c
|
r96: min_cnt still wrong in chaining
|
2017-06-28 11:03:03 -04:00 |
|
Heng Li
|
b696d5fe5e
|
disable kalloc in the debugging mode
|
2017-06-28 10:50:27 -04:00 |
|
Heng Li
|
bf0e8199e2
|
r94: min_cnt is tested in a wrong way in chain
|
2017-06-28 10:39:27 -04:00 |
|
Heng Li
|
bcd9b1c621
|
r93: fixed various small issues
|
2017-06-28 10:35:21 -04:00 |
|
Heng Li
|
cdc2a1e29f
|
r92: fixed a bug for overlapping alignment
On the PBcR example E. coli reads, miniasm gives one circular unitig.
|
2017-06-27 22:03:31 -04:00 |
|
Heng Li
|
51057ab673
|
expose scoring
|
2017-06-27 21:37:25 -04:00 |
|
Heng Li
|
533150d49d
|
r90: revert default band width to 1000
10000 is excessively tolerant with bad hits.
|
2017-06-27 20:29:39 -04:00 |
|
Heng Li
|
fa80177e58
|
r89: added minimal number of minimizer counts
|
2017-06-27 18:43:15 -04:00 |
|
Heng Li
|
8977f07269
|
r88: fixed an out-of-boundary bug in ksw2
|
2017-06-27 14:50:31 -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
|
490a37a599
|
number of allocated units must be an even number
|
2017-06-26 23:15:30 -04:00 |
|
Heng Li
|
0d03a43efd
|
don't round to power-of-2
Because rounding wastes memory when we use power-of-2 high-water marks.
|
2017-06-26 22:10:45 -04:00 |
|
Heng Li
|
b56cd790f6
|
enabled kalloc (was a mistake)
Not using kalloc leads to significant malloc overhead.
|
2017-06-26 15:41:55 -04:00 |
|
Heng Li
|
99c57b86c5
|
r79: drop bad hits
|
2017-06-26 15:28:04 -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
|
10644f2165
|
r76: missing header file
|
2017-06-26 12:36:37 -04:00 |
|
Heng Li
|
4b8e88a5f4
|
use long options
|
2017-06-26 12:31:36 -04:00 |
|
Heng Li
|
640b1a1727
|
command-line option to control CIGAR output
|
2017-06-26 11:41:09 -04:00 |
|
Heng Li
|
24d7f7f8b1
|
disabled dynamic banding; buggy
|
2017-06-25 22:43:15 -04:00 |
|
Heng Li
|
b1077ff14c
|
sam output
|
2017-06-25 22:05:20 -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
|
0c274280ae
|
output the original score
|
2017-06-23 22:56:50 -04:00 |
|
Heng Li
|
2987be288c
|
output cigar
|
2017-06-23 22:53:47 -04:00 |
|
Heng Li
|
35b84f88c6
|
backup
|
2017-06-23 22:42:15 -04:00 |
|
Heng Li
|
523a8832ad
|
backup
|
2017-06-23 20:57:17 -04:00 |
|
Heng Li
|
7ed26a4857
|
backup
|
2017-06-23 19:31:23 -04:00 |
|
Heng Li
|
d75b5b4e8a
|
backup; NOT working yet
|
2017-06-23 19:21:47 -04:00 |
|
Heng Li
|
4fea3d778a
|
backup
|
2017-06-23 18:57:00 -04:00 |
|
Heng Li
|
6c8368c24c
|
get the left-extension sequence correctly
|
2017-06-23 18:25:47 -04:00 |
|
Heng Li
|
990f7b0b71
|
backup
|
2017-06-23 15:13:53 -04:00 |
|
Heng Li
|
4ae0b46972
|
min_ksw_len
|
2017-06-23 14:38:28 -04:00 |
|
Heng Li
|
9cd313eae1
|
sequence retrieval working
|
2017-06-23 14:11:56 -04:00 |