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 |
|
Heng Li
|
d11049eb32
|
r120: use max-scoring seg to control output
much better now
|
2017-06-30 14:21:44 -04:00 |
|
Heng Li
|
08a61c3cfc
|
r119: fixed a bug hidden by a previous bug
|
2017-06-30 13:27:47 -04:00 |
|
Heng Li
|
1a903486b9
|
r118: bugfix - regs unsorted before filtering
|
2017-06-30 12:52:28 -04:00 |
|
Heng Li
|
5dcd8f8965
|
r117: fixed a bug in logic
|
2017-06-30 11:52:42 -04:00 |
|
Heng Li
|
91e1c4d6db
|
r116: fixed another bug caused by refactoring
|
2017-06-30 00:03:45 -04:00 |
|
Heng Li
|
52b4d8e2c9
|
r115: set primary tag; still buggy
|
2017-06-29 23:48:35 -04:00 |
|
Heng Li
|
c4871f380c
|
r114: make SAM output better
|
2017-06-29 23:08:41 -04:00 |
|
Heng Li
|
03267e8fa7
|
r113: fixed a sam header bug
|
2017-06-29 22:43:06 -04:00 |
|
Heng Li
|
11167f511b
|
r112: output z-drop
|
2017-06-29 22:08:46 -04:00 |
|
Heng Li
|
3825feeeac
|
r111: changed the default z-drop to 200
|
2017-06-29 21:37:56 -04:00 |
|
Heng Li
|
e2b86d0332
|
r110: fixed a bug caused by refactoring
|
2017-06-29 21:12:31 -04:00 |
|
Heng Li
|
08cbb09fcc
|
r109: changed the default scoring
|
2017-06-29 20:21:57 -04:00 |
|
Heng Li
|
4cd456b9ba
|
r108: refactoring, move reg1 routines to hit.c
|
2017-06-29 19:44:11 -04:00 |
|
Heng Li
|
ecedfe5788
|
code refactoring for mm_reg1_t
|
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
|
337c2a21cd
|
r105: fixed a bug in repeated right ext when zdrop
|
2017-06-29 15:45:07 -04:00 |
|
Heng Li
|
b9075d39a8
|
r104: long gap patching
|
2017-06-29 14:54:54 -04:00 |
|
Heng Li
|
17944a75c2
|
merge into map.c
|
2017-06-29 14:20:14 -04:00 |
|
Heng Li
|
d274e1b743
|
backup
|
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
|
2017-06-28 23:56:33 -04:00 |
|
Heng Li
|
cf703655cb
|
optional sse4
|
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
|
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 |