 Heng Li
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53c4bf5e4f
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r149: introduced debugging flags on CLI
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2017-07-03 11:02:32 -04:00 |
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Heng Li
|
2e4fd9f1d0
|
r148: revamped regs handling after cigar
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2017-07-03 10:44:26 -04:00 |
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Heng Li
|
696ebce66e
|
backup; still buggy
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2017-07-03 00:52:00 -04:00 |
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Heng Li
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e06c342659
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r146: in filtering, drop children if parent out
This has been causing several segfaults.
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2017-07-03 00:28:12 -04:00 |
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Heng Li
|
51cfb60520
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r145: changed default -p from 2 to 0.8
For long reads, secondary alignments can be very information.
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2017-07-02 22:51:45 -04:00 |
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Heng Li
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632b8638d2
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r144: adjust primary aln after cigar
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2017-07-02 22:43:02 -04:00 |
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Heng Li
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2b45ba7a0b
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r143: fixed a segfault and incorrect .parent
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2017-07-02 19:56:21 -04:00 |
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Heng Li
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74d306a596
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fixed bug when retaining 2ndary aln; still buggy
|
2017-07-02 19:08:30 -04:00 |
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Heng Li
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da90b614db
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r141: replaced -b with -a (for SAM output)
-b sounds like BAM. I like -a better.
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2017-07-01 16:54:59 -04:00 |
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Heng Li
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67cad9dff3
|
added limitations
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2017-07-01 12:11:56 -04:00 |
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Heng Li
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a92bd75b7b
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make the table fit 80 columns
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2017-07-01 11:54:07 -04:00 |
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Heng Li
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02145b2166
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explain option -d
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2017-07-01 11:48:37 -04:00 |
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Heng Li
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3c45d84012
|
added license
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2017-07-01 11:39:19 -04:00 |
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Heng Li
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b2ce3f9ed0
|
get rid of two more new lines
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2017-07-01 11:37:58 -04:00 |
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Heng Li
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5ebe868db5
|
added two more new lines
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2017-07-01 11:32:49 -04:00 |
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Heng Li
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cb6c277c62
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removed unnecessary empty lines
On linux, these empty lines count.
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2017-07-01 11:31:32 -04:00 |
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Heng Li
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b883d132e2
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no effective change
|
2017-07-01 11:26:23 -04:00 |
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Heng Li
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2338e887d9
|
finished the first draft of manpage
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2017-07-01 11:25:54 -04:00 |
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Heng Li
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a9f089f0aa
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r131: wrong EOF test; make mb_size <= batch_size
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2017-07-01 09:26:09 -04:00 |
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Heng Li
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d4301736b8
|
more manpage
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2017-07-01 00:23:46 -04:00 |
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Heng Li
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41efd03d7a
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r129: fixed memory leak caused by qualities
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2017-06-30 23:48:00 -04:00 |
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Heng Li
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10910b72d1
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backup
|
2017-06-30 23:31:38 -04:00 |
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Heng Li
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d118cafd25
|
added man page
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2017-06-30 23:30:17 -04:00 |
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Heng Li
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426c2975f6
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r126: filter by fraction of seed coverage
otherwise we may get too many poor overlap mappings.
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2017-06-30 22:15:45 -04:00 |
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Heng Li
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d73bb28097
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r125: changed CLI options
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2017-06-30 19:08:47 -04:00 |
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Heng Li
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b08591c7a0
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r124: a bit better CLI prompt
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2017-06-30 15:46:52 -04:00 |
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Heng Li
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3a5486325a
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r123: fixed a mem leak; more presets
|
2017-06-30 15:39:05 -04:00 |
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Heng Li
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646a746cdc
|
r122: filter contained aln after DP extension
|
2017-06-30 15:23:30 -04:00 |
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Heng Li
|
fce87ce7bd
|
r121: output QUAL and unmapped to SAM
|
2017-06-30 14:40:54 -04:00 |
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Heng Li
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d11049eb32
|
r120: use max-scoring seg to control output
much better now
|
2017-06-30 14:21:44 -04:00 |
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Heng Li
|
08a61c3cfc
|
r119: fixed a bug hidden by a previous bug
|
2017-06-30 13:27:47 -04:00 |
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Heng Li
|
1a903486b9
|
r118: bugfix - regs unsorted before filtering
|
2017-06-30 12:52:28 -04:00 |
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Heng Li
|
5dcd8f8965
|
r117: fixed a bug in logic
|
2017-06-30 11:52:42 -04:00 |
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Heng Li
|
91e1c4d6db
|
r116: fixed another bug caused by refactoring
|
2017-06-30 00:03:45 -04:00 |
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|
Heng Li
|
52b4d8e2c9
|
r115: set primary tag; still buggy
|
2017-06-29 23:48:35 -04:00 |
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Heng Li
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c4871f380c
|
r114: make SAM output better
|
2017-06-29 23:08:41 -04:00 |
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|
Heng Li
|
03267e8fa7
|
r113: fixed a sam header bug
|
2017-06-29 22:43:06 -04:00 |
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|
Heng Li
|
11167f511b
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r112: output z-drop
|
2017-06-29 22:08:46 -04:00 |
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Heng Li
|
3825feeeac
|
r111: changed the default z-drop to 200
|
2017-06-29 21:37:56 -04:00 |
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|
Heng Li
|
e2b86d0332
|
r110: fixed a bug caused by refactoring
|
2017-06-29 21:12:31 -04:00 |
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|
Heng Li
|
08cbb09fcc
|
r109: changed the default scoring
|
2017-06-29 20:21:57 -04:00 |
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|
Heng Li
|
4cd456b9ba
|
r108: refactoring, move reg1 routines to hit.c
|
2017-06-29 19:44:11 -04:00 |
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|
Heng Li
|
ecedfe5788
|
code refactoring for mm_reg1_t
|
2017-06-29 19:35:38 -04:00 |
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|
Heng Li
|
cc67f1b781
|
compute mapq; not working for z-split yet
|
2017-06-29 17:52:48 -04:00 |
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Heng Li
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337c2a21cd
|
r105: fixed a bug in repeated right ext when zdrop
|
2017-06-29 15:45:07 -04:00 |
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|
Heng Li
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b9075d39a8
|
r104: long gap patching
|
2017-06-29 14:54:54 -04:00 |
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|
Heng Li
|
17944a75c2
|
merge into map.c
|
2017-06-29 14:20:14 -04:00 |
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|
Heng Li
|
d274e1b743
|
backup
|
2017-06-29 12:58:52 -04:00 |
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|
Heng Li
|
c8d122bcdb
|
backup
|
2017-06-29 11:11:15 -04:00 |
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|
Heng Li
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9fbf7e41e1
|
r99: report progress
|
2017-06-28 23:56:33 -04:00 |
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Heng Li
|
cf703655cb
|
optional sse4
|
2017-06-28 22:21:52 -04:00 |
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Heng Li
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38070e8a05
|
r98: fixed segfault for certain scoring
due to unsigned comparisons between -1 and chromosome length
|
2017-06-28 22:18:51 -04:00 |
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|
Heng Li
|
5e202afb5f
|
fixed invalid backtracking, a temporary solution
|
2017-06-28 18:17:57 -04:00 |
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Heng Li
|
a25866c25c
|
r96: min_cnt still wrong in chaining
|
2017-06-28 11:03:03 -04:00 |
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Heng Li
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b696d5fe5e
|
disable kalloc in the debugging mode
|
2017-06-28 10:50:27 -04:00 |
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Heng Li
|
bf0e8199e2
|
r94: min_cnt is tested in a wrong way in chain
|
2017-06-28 10:39:27 -04:00 |
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|
Heng Li
|
bcd9b1c621
|
r93: fixed various small issues
|
2017-06-28 10:35:21 -04:00 |
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|
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 |
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Heng Li
|
51057ab673
|
expose scoring
|
2017-06-27 21:37:25 -04:00 |
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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 |
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Heng Li
|
fa80177e58
|
r89: added minimal number of minimizer counts
|
2017-06-27 18:43:15 -04:00 |
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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 |
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|
Heng Li
|
734028f92b
|
validate z-drop
|
2017-06-27 11:25:39 -04:00 |
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Heng Li
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c02ff4662c
|
r85: two-round z-drop
|
2017-06-27 10:36:24 -04:00 |
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|
Heng Li
|
490a37a599
|
number of allocated units must be an even number
|
2017-06-26 23:15:30 -04:00 |
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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 |
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Heng Li
|
b56cd790f6
|
enabled kalloc (was a mistake)
Not using kalloc leads to significant malloc overhead.
|
2017-06-26 15:41:55 -04:00 |
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Heng Li
|
99c57b86c5
|
r79: drop bad hits
|
2017-06-26 15:28:04 -04:00 |
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|
Heng Li
|
5b614ae828
|
r78: fixed a split bug
|
2017-06-26 14:45:23 -04:00 |
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|
Heng Li
|
de54c9dac2
|
r77: fixed an index loading bug (offset not set)
|
2017-06-26 13:56:25 -04:00 |
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|
Heng Li
|
10644f2165
|
r76: missing header file
|
2017-06-26 12:36:37 -04:00 |
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|
Heng Li
|
4b8e88a5f4
|
use long options
|
2017-06-26 12:31:36 -04:00 |
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|
Heng Li
|
640b1a1727
|
command-line option to control CIGAR output
|
2017-06-26 11:41:09 -04:00 |
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|
Heng Li
|
24d7f7f8b1
|
disabled dynamic banding; buggy
|
2017-06-25 22:43:15 -04:00 |
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|
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 |
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|
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 |
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|
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 |
|
|
Heng Li
|
326d91deb0
|
backup
|
2017-06-23 14:06:00 -04:00 |
|