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 |
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Heng Li
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10910b72d1
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backup
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2017-06-30 23:31:38 -04:00 |
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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 |
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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 |
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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 |
|
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 |
|
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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11167f511b
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r112: output z-drop
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2017-06-29 22:08:46 -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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e2b86d0332
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r110: fixed a bug caused by refactoring
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2017-06-29 21:12:31 -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
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r108: refactoring, move reg1 routines to hit.c
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2017-06-29 19:44:11 -04:00 |
|
Heng Li
|
ecedfe5788
|
code refactoring for mm_reg1_t
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2017-06-29 19:35:38 -04:00 |
|
Heng Li
|
cc67f1b781
|
compute mapq; not working for z-split yet
|
2017-06-29 17:52:48 -04:00 |
|
Heng Li
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337c2a21cd
|
r105: fixed a bug in repeated right ext when zdrop
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2017-06-29 15:45:07 -04:00 |
|
Heng Li
|
b9075d39a8
|
r104: long gap patching
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2017-06-29 14:54:54 -04:00 |
|
Heng Li
|
17944a75c2
|
merge into map.c
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2017-06-29 14:20:14 -04:00 |
|
Heng Li
|
d274e1b743
|
backup
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2017-06-29 12:58:52 -04:00 |
|
Heng Li
|
c8d122bcdb
|
backup
|
2017-06-29 11:11:15 -04:00 |
|
Heng Li
|
9fbf7e41e1
|
r99: report progress
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2017-06-28 23:56:33 -04:00 |
|
Heng Li
|
cf703655cb
|
optional sse4
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2017-06-28 22:21:52 -04:00 |
|
Heng Li
|
38070e8a05
|
r98: fixed segfault for certain scoring
due to unsigned comparisons between -1 and chromosome length
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2017-06-28 22:18:51 -04:00 |
|
Heng Li
|
5e202afb5f
|
fixed invalid backtracking, a temporary solution
|
2017-06-28 18:17:57 -04:00 |
|
Heng Li
|
a25866c25c
|
r96: min_cnt still wrong in chaining
|
2017-06-28 11:03:03 -04:00 |
|
Heng Li
|
b696d5fe5e
|
disable kalloc in the debugging mode
|
2017-06-28 10:50:27 -04:00 |
|
Heng Li
|
bf0e8199e2
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r94: min_cnt is tested in a wrong way in chain
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2017-06-28 10:39:27 -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.
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2017-06-27 22:03:31 -04:00 |