Heng Li
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b696d5fe5e
|
disable kalloc in the debugging mode
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2017-06-28 10:50:27 -04:00 |
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Heng Li
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bcd9b1c621
|
r93: fixed various small issues
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2017-06-28 10:35:21 -04:00 |
|
Heng Li
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cdc2a1e29f
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r92: fixed a bug for overlapping alignment
On the PBcR example E. coli reads, miniasm gives one circular unitig.
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2017-06-27 22:03:31 -04:00 |
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Heng Li
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533150d49d
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r90: revert default band width to 1000
10000 is excessively tolerant with bad hits.
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2017-06-27 20:29:39 -04:00 |
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Heng Li
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fa80177e58
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r89: added minimal number of minimizer counts
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2017-06-27 18:43:15 -04:00 |
|
Heng Li
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99c57b86c5
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r79: drop bad hits
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2017-06-26 15:28:04 -04:00 |
|
Heng Li
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5b614ae828
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r78: fixed a split bug
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2017-06-26 14:45:23 -04:00 |
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Heng Li
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de54c9dac2
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r77: fixed an index loading bug (offset not set)
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2017-06-26 13:56:25 -04:00 |
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Heng Li
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640b1a1727
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command-line option to control CIGAR output
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2017-06-26 11:41:09 -04:00 |
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Heng Li
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b1077ff14c
|
sam output
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2017-06-25 22:05:20 -04:00 |
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Heng Li
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39083be9ab
|
separated formating printing
for SAM in future; and for performance
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2017-06-25 16:13:54 -04:00 |
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Heng Li
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f20d550a59
|
fixed the NM bug
due to reversed CIGAR
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2017-06-25 11:24:39 -04:00 |
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Heng Li
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ef5dd318ca
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implemented chain splitting; NOT tested!!!
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2017-06-24 22:57:43 -04:00 |
|
Heng Li
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aa5881e7bb
|
backup
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2017-06-24 22:51:31 -04:00 |
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Heng Li
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2d8fda9586
|
an alternative strategy to fix for HPC
it makes the result better, but still not quite right.
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2017-06-24 09:26:24 -04:00 |
|
Heng Li
|
0c274280ae
|
output the original score
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2017-06-23 22:56:50 -04:00 |
|
Heng Li
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2987be288c
|
output cigar
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2017-06-23 22:53:47 -04:00 |
|
Heng Li
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35b84f88c6
|
backup
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2017-06-23 22:42:15 -04:00 |
|
Heng Li
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d75b5b4e8a
|
backup; NOT working yet
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2017-06-23 19:21:47 -04:00 |
|
Heng Li
|
990f7b0b71
|
backup
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2017-06-23 15:13:53 -04:00 |
|
Heng Li
|
4ae0b46972
|
min_ksw_len
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2017-06-23 14:38:28 -04:00 |
|
Heng Li
|
44cdd18de0
|
start to work on alignment
|
2017-06-23 13:44:45 -04:00 |
|
Heng Li
|
372698bb23
|
disable k-mer intersection for now
My current focus is long-read mapping. This functionality is not needed right now.
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2017-06-11 14:13:41 -04:00 |
|
Heng Li
|
b04e4b9215
|
r36: bring back primary; don't output all mappings
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2017-06-08 15:28:19 -04:00 |
|
Heng Li
|
6c099bef89
|
removed some debugging code
not necessary when we can print PAF
|
2017-06-07 14:49:11 -04:00 |
|
Heng Li
|
be9a7f4e41
|
removed the old print code
|
2017-06-07 14:24:31 -04:00 |
|
Heng Li
|
8ad5cfde42
|
output PAF
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2017-06-07 14:18:32 -04:00 |
|
Heng Li
|
c01f2dd757
|
fixed a bug
|
2017-06-07 11:40:13 -04:00 |
|
Heng Li
|
c1c946aa67
|
fixed memory leaks
though some of them are not really leaks when kalloc is in use.
|
2017-06-06 21:45:55 -04:00 |
|
Heng Li
|
e6adb673f9
|
fixed a stupid bug
|
2017-06-06 15:45:42 -04:00 |
|
Heng Li
|
a2958a4836
|
minor tweaks
|
2017-06-06 15:31:21 -04:00 |
|
Heng Li
|
6d4348db44
|
dp chaining mostly works, but fails sometimes
which means there are bugs that need to be fixed
|
2017-06-06 14:19:50 -04:00 |
|
Heng Li
|
1a9fc04cf0
|
backup
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2017-06-06 10:16:33 -04:00 |
|
Heng Li
|
acc7382a30
|
backup
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2017-06-04 16:09:45 -04:00 |
|
Heng Li
|
949d9be872
|
chaining with DP
|
2017-05-09 22:20:57 +08:00 |
|
Heng Li
|
2827c29b48
|
minor backup
|
2017-05-04 23:22:11 +08:00 |
|
Heng Li
|
10db6b0434
|
wrong HPC
|
2017-05-04 17:45:19 +08:00 |
|
Heng Li
|
06adabd0dc
|
clean bill from valgrind
|
2017-05-04 12:44:49 +08:00 |
|
Heng Li
|
7b53f7aa84
|
chaining
|
2017-05-03 20:47:29 +08:00 |
|
Heng Li
|
f2ae8eb670
|
mostly debugging code
|
2017-05-01 16:50:09 +08:00 |
|
Heng Li
|
2c9f1bce3e
|
k-mer thinning apparently working
|
2017-04-28 18:24:45 +08:00 |
|
Heng Li
|
7b7fabef4d
|
added idx_stat
|
2017-04-26 22:52:28 +08:00 |
|
Heng Li
|
de367a340c
|
compilable again
|
2017-04-26 19:36:46 +08:00 |
|
Heng Li
|
1bf3ae6752
|
backup
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2017-04-09 15:09:39 -04:00 |
|
Heng Li
|
79c9478f46
|
backup
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2017-04-09 14:59:39 -04:00 |
|
Heng Li
|
8c230563cc
|
can be compiled
|
2017-04-07 15:56:10 -04:00 |