Heng Li
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53c4bf5e4f
|
r149: introduced debugging flags on CLI
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2017-07-03 11:02:32 -04:00 |
|
Heng Li
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2e4fd9f1d0
|
r148: revamped regs handling after cigar
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2017-07-03 10:44:26 -04:00 |
|
Heng Li
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51cfb60520
|
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 |
|
Heng Li
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74d306a596
|
fixed bug when retaining 2ndary aln; still buggy
|
2017-07-02 19:08:30 -04:00 |
|
Heng Li
|
41efd03d7a
|
r129: fixed memory leak caused by qualities
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2017-06-30 23:48:00 -04:00 |
|
Heng Li
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426c2975f6
|
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 |
|
Heng Li
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646a746cdc
|
r122: filter contained aln after DP extension
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2017-06-30 15:23:30 -04:00 |
|
Heng Li
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fce87ce7bd
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r121: output QUAL and unmapped to SAM
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2017-06-30 14:40:54 -04:00 |
|
Heng Li
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d11049eb32
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r120: use max-scoring seg to control output
much better now
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2017-06-30 14:21:44 -04:00 |
|
Heng Li
|
1a903486b9
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r118: bugfix - regs unsorted before filtering
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2017-06-30 12:52:28 -04:00 |
|
Heng Li
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03267e8fa7
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r113: fixed a sam header bug
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2017-06-29 22:43:06 -04:00 |
|
Heng Li
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3825feeeac
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r111: changed the default z-drop to 200
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2017-06-29 21:37:56 -04:00 |
|
Heng Li
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08cbb09fcc
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r109: changed the default scoring
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2017-06-29 20:21:57 -04:00 |
|
Heng Li
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4cd456b9ba
|
r108: refactoring, move reg1 routines to hit.c
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2017-06-29 19:44:11 -04:00 |
|
Heng Li
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ecedfe5788
|
code refactoring for mm_reg1_t
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2017-06-29 19:35:38 -04:00 |
|
Heng Li
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cc67f1b781
|
compute mapq; not working for z-split yet
|
2017-06-29 17:52:48 -04:00 |
|
Heng Li
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b9075d39a8
|
r104: long gap patching
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2017-06-29 14:54:54 -04:00 |
|
Heng Li
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17944a75c2
|
merge into map.c
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2017-06-29 14:20:14 -04:00 |
|
Heng Li
|
c8d122bcdb
|
backup
|
2017-06-29 11:11:15 -04:00 |
|
Heng Li
|
9fbf7e41e1
|
r99: report progress
|
2017-06-28 23:56:33 -04:00 |
|
Heng Li
|
b696d5fe5e
|
disable kalloc in the debugging mode
|
2017-06-28 10:50:27 -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
|
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
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fa80177e58
|
r89: added minimal number of minimizer counts
|
2017-06-27 18:43:15 -04:00 |
|
Heng Li
|
99c57b86c5
|
r79: drop bad hits
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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
|
640b1a1727
|
command-line option to control CIGAR output
|
2017-06-26 11:41:09 -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
|
f20d550a59
|
fixed the NM bug
due to reversed CIGAR
|
2017-06-25 11:24:39 -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
|
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
|
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
|
d75b5b4e8a
|
backup; NOT working yet
|
2017-06-23 19:21:47 -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
|
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.
|
2017-06-11 14:13:41 -04:00 |
|
Heng Li
|
b04e4b9215
|
r36: bring back primary; don't output all mappings
|
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
|
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 |