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108 Commits 9 Branches 35 Tags
08cbb09fcc2c6292bc9cfe9dc87dca19fc951b46
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108 Commits

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Author SHA1 Message Date
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
Heng Li
b696d5fe5e disable kalloc in the debugging mode 2017-06-28 10:50:27 -04:00
Heng Li
bf0e8199e2 r94: min_cnt is tested in a wrong way in chain 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.
 2017-06-27 22:03:31 -04:00
Heng Li
51057ab673 expose scoring 2017-06-27 21:37:25 -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
fa80177e58 r89: added minimal number of minimizer counts 2017-06-27 18:43:15 -04:00
Heng Li
8977f07269 r88: fixed an out-of-boundary bug in ksw2 2017-06-27 14:50:31 -04:00
Heng Li
42283ef10c r87: fixed a bug in ksw2 2017-06-27 13:29:48 -04:00
Heng Li
734028f92b validate z-drop 2017-06-27 11:25:39 -04:00
Heng Li
c02ff4662c r85: two-round z-drop 2017-06-27 10:36:24 -04:00
Heng Li
490a37a599 number of allocated units must be an even number 2017-06-26 23:15:30 -04:00
Heng Li
0d03a43efd don't round to power-of-2 
Because rounding wastes memory when we use power-of-2 high-water marks.
 2017-06-26 22:10:45 -04:00
Heng Li
b56cd790f6 enabled kalloc (was a mistake) 
Not using kalloc leads to significant malloc overhead.
 2017-06-26 15:41:55 -04:00
Heng Li
99c57b86c5 r79: drop bad hits 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
10644f2165 r76: missing header file 2017-06-26 12:36:37 -04:00
Heng Li
4b8e88a5f4 use long options 2017-06-26 12:31:36 -04:00
Heng Li
640b1a1727 command-line option to control CIGAR output 2017-06-26 11:41:09 -04:00
Heng Li
24d7f7f8b1 disabled dynamic banding; buggy 2017-06-25 22:43:15 -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
7780ab792a removed some comment lines 2017-06-25 11:53:35 -04:00
Heng Li
56364200c8 avoid contained hits due to split 2017-06-25 11:43:50 -04:00
Heng Li
f20d550a59 fixed the NM bug 
due to reversed CIGAR
 2017-06-25 11:24:39 -04:00
Heng Li
b261a4a74b zdrop sort of works, but has issues 
left and right extensions are different; NM is also wrong
 2017-06-25 10:52:14 -04:00
Heng Li
72dfb0c99e fixed a bug in ksw2 2017-06-25 10:22:13 -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
d08b58d21f minor 2017-06-24 19:33:59 -04:00
Heng Li
672782f03a simplified hp_len a little 2017-06-24 19:27:58 -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
6088dc11ff wrong SW score 2017-06-23 23:24:49 -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