Heng Li
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3f6a0b0b5c
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r162: improved chaining accuracy
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2017-07-08 14:29:36 -04:00 |
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Heng Li
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38b2830e18
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r161: filter bad seeds; changed default -g/-r
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2017-07-08 13:31:27 -04:00 |
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Heng Li
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1fee5f8edc
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r160: -O and -E accept two numbers
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2017-07-08 11:34:52 -04:00 |
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Heng Li
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cc554aee43
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r159: use two-piece gap penalty
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2017-07-08 10:26:00 -04:00 |
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Heng Li
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9823317e8f
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r158: optionally ignore base quality
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2017-07-05 18:23:50 -04:00 |
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Heng Li
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d1f518e3ca
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for clarity
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2017-07-04 11:56:50 -04:00 |
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Heng Li
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6b584a1235
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added README
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2017-07-04 11:47:29 -04:00 |
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Heng Li
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8fff901e53
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added test data
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2017-07-04 10:56:48 -04:00 |
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Heng Li
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a65e557a7c
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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
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r153: sam primary record not set sometimes
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2017-07-03 13:18:57 -04:00 |
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Heng Li
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6ead8af104
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Merge branch 'dev' into 'master'
Fixed bugs when reporting secondary alignments
See merge request !1
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2017-07-03 16:17:08 +00:00 |
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Heng Li
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a94bc31311
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r151: documentations
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2017-07-03 12:11:07 -04:00 |
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Heng Li
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b625247300
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r150: mm_sync_regs() doesn't work with negative id
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2017-07-03 11:36:34 -04:00 |
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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
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2e4fd9f1d0
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r148: revamped regs handling after cigar
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2017-07-03 10:44:26 -04:00 |
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Heng Li
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696ebce66e
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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
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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
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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
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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
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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
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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
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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
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2017-07-01 11:26:23 -04:00 |
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Heng Li
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2338e887d9
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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
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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 |
|
Heng Li
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10910b72d1
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backup
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2017-06-30 23:31:38 -04:00 |
|
Heng Li
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d118cafd25
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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
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2017-06-30 15:39:05 -04:00 |
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Heng Li
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646a746cdc
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r122: filter contained aln after DP extension
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2017-06-30 15:23:30 -04:00 |
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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
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08a61c3cfc
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r119: fixed a bug hidden by a previous bug
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2017-06-30 13:27:47 -04:00 |
|
Heng Li
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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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5dcd8f8965
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r117: fixed a bug in logic
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2017-06-30 11:52:42 -04:00 |
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Heng Li
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91e1c4d6db
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r116: fixed another bug caused by refactoring
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2017-06-30 00:03:45 -04:00 |
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Heng Li
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52b4d8e2c9
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r115: set primary tag; still buggy
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2017-06-29 23:48:35 -04:00 |
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Heng Li
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c4871f380c
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r114: make SAM output better
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2017-06-29 23:08:41 -04:00 |
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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 |