Heng Li
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826c8ba892
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r170: added a debugging flag
something wrong with chaining
|
2017-07-11 14:47:35 -04:00 |
|
Heng Li
|
801bc84b01
|
r169: output more accurate col. 10&11 to PAF
In r168, col.10 is smaller than what it should be. This confuses miniasm.
|
2017-07-11 14:09:51 -04:00 |
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Heng Li
|
782449975d
|
r168: fixed a bug in long join: a[] not sorted
Also added length requirement for long join and changed -g in the ava mode
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2017-07-09 12:14:20 -04:00 |
|
Heng Li
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1ac48556ae
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r167: long join threshold depends on gap
also caught a bug for reverse strand join
|
2017-07-09 10:38:51 -04:00 |
|
Heng Li
|
34ed85d46a
|
optionally print the postions of long indels
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2017-07-08 20:16:25 -04:00 |
|
Heng Li
|
2f11a63b22
|
script to collect alignment stats
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2017-07-08 20:01:36 -04:00 |
|
Heng Li
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4ee3202539
|
r164: unmapped read not properly flagged
|
2017-07-08 18:16:18 -04:00 |
|
Heng Li
|
42846ce65d
|
r163: reduced long join score requirement
because the chaining score is generally smaller with the last few commits.
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2017-07-08 15:51:52 -04:00 |
|
Heng Li
|
3f6a0b0b5c
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r162: improved chaining accuracy
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2017-07-08 14:29:36 -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
|
1fee5f8edc
|
r160: -O and -E accept two numbers
|
2017-07-08 11:34:52 -04:00 |
|
Heng Li
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cc554aee43
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r159: use two-piece gap penalty
|
2017-07-08 10:26:00 -04:00 |
|
Heng Li
|
9823317e8f
|
r158: optionally ignore base quality
|
2017-07-05 18:23:50 -04:00 |
|
Heng Li
|
d1f518e3ca
|
for clarity
|
2017-07-04 11:56:50 -04:00 |
|
Heng Li
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6b584a1235
|
added README
|
2017-07-04 11:47:29 -04:00 |
|
Heng Li
|
8fff901e53
|
added test data
|
2017-07-04 10:56:48 -04:00 |
|
Heng Li
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a65e557a7c
|
Merge branch 'dev'
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2017-07-03 13:19:17 -04:00 |
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Heng Li
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e07daad7ad
|
r153: sam primary record not set sometimes
|
2017-07-03 13:18:57 -04:00 |
|
Heng Li
|
6ead8af104
|
Merge branch 'dev' into 'master'
Fixed bugs when reporting secondary alignments
See merge request !1
|
2017-07-03 16:17:08 +00:00 |
|
Heng Li
|
a94bc31311
|
r151: documentations
|
2017-07-03 12:11:07 -04:00 |
|
Heng Li
|
b625247300
|
r150: mm_sync_regs() doesn't work with negative id
|
2017-07-03 11:36:34 -04:00 |
|
Heng Li
|
53c4bf5e4f
|
r149: introduced debugging flags on CLI
|
2017-07-03 11:02:32 -04:00 |
|
Heng Li
|
2e4fd9f1d0
|
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
|
e06c342659
|
r146: in filtering, drop children if parent out
This has been causing several segfaults.
|
2017-07-03 00:28:12 -04:00 |
|
Heng Li
|
51cfb60520
|
r145: changed default -p from 2 to 0.8
For long reads, secondary alignments can be very information.
|
2017-07-02 22:51:45 -04:00 |
|
Heng Li
|
632b8638d2
|
r144: adjust primary aln after cigar
|
2017-07-02 22:43:02 -04:00 |
|
Heng Li
|
2b45ba7a0b
|
r143: fixed a segfault and incorrect .parent
|
2017-07-02 19:56:21 -04:00 |
|
Heng Li
|
74d306a596
|
fixed bug when retaining 2ndary aln; still buggy
|
2017-07-02 19:08:30 -04:00 |
|
Heng Li
|
da90b614db
|
r141: replaced -b with -a (for SAM output)
-b sounds like BAM. I like -a better.
|
2017-07-01 16:54:59 -04:00 |
|
Heng Li
|
67cad9dff3
|
added limitations
|
2017-07-01 12:11:56 -04:00 |
|
Heng Li
|
a92bd75b7b
|
make the table fit 80 columns
|
2017-07-01 11:54:07 -04:00 |
|
Heng Li
|
02145b2166
|
explain option -d
|
2017-07-01 11:48:37 -04:00 |
|
Heng Li
|
3c45d84012
|
added license
|
2017-07-01 11:39:19 -04:00 |
|
Heng Li
|
b2ce3f9ed0
|
get rid of two more new lines
|
2017-07-01 11:37:58 -04:00 |
|
Heng Li
|
5ebe868db5
|
added two more new lines
|
2017-07-01 11:32:49 -04:00 |
|
Heng Li
|
cb6c277c62
|
removed unnecessary empty lines
On linux, these empty lines count.
|
2017-07-01 11:31:32 -04:00 |
|
Heng Li
|
b883d132e2
|
no effective change
|
2017-07-01 11:26:23 -04:00 |
|
Heng Li
|
2338e887d9
|
finished the first draft of manpage
|
2017-07-01 11:25:54 -04:00 |
|
Heng Li
|
a9f089f0aa
|
r131: wrong EOF test; make mb_size <= batch_size
|
2017-07-01 09:26:09 -04:00 |
|
Heng Li
|
d4301736b8
|
more manpage
|
2017-07-01 00:23:46 -04:00 |
|
Heng Li
|
41efd03d7a
|
r129: fixed memory leak caused by qualities
|
2017-06-30 23:48:00 -04:00 |
|
Heng Li
|
10910b72d1
|
backup
|
2017-06-30 23:31:38 -04:00 |
|
Heng Li
|
d118cafd25
|
added man page
|
2017-06-30 23:30:17 -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
|
d73bb28097
|
r125: changed CLI options
|
2017-06-30 19:08:47 -04:00 |
|
Heng Li
|
b08591c7a0
|
r124: a bit better CLI prompt
|
2017-06-30 15:46:52 -04:00 |
|
Heng Li
|
3a5486325a
|
r123: fixed a mem leak; more presets
|
2017-06-30 15:39:05 -04:00 |
|
Heng Li
|
646a746cdc
|
r122: filter contained aln after DP extension
|
2017-06-30 15:23:30 -04:00 |
|
Heng Li
|
fce87ce7bd
|
r121: output QUAL and unmapped to SAM
|
2017-06-30 14:40:54 -04:00 |