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108 Commits 9 Branches 35 Tags
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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
Heng Li 35b84f88c6 backup 2017-06-23 22:42:15 -04:00
Heng Li 523a8832ad backup 2017-06-23 20:57:17 -04:00
Heng Li 7ed26a4857 backup 2017-06-23 19:31:23 -04:00
Heng Li d75b5b4e8a backup; NOT working yet 2017-06-23 19:21:47 -04:00
Heng Li 4fea3d778a backup 2017-06-23 18:57:00 -04:00
Heng Li 6c8368c24c get the left-extension sequence correctly 2017-06-23 18:25:47 -04:00
Heng Li 990f7b0b71 backup 2017-06-23 15:13:53 -04:00
Heng Li 4ae0b46972 min_ksw_len 2017-06-23 14:38:28 -04:00
Heng Li 9cd313eae1 sequence retrieval working 2017-06-23 14:11:56 -04:00
Heng Li 326d91deb0 backup 2017-06-23 14:06:00 -04:00
Heng Li 44cdd18de0 start to work on alignment 2017-06-23 13:44:45 -04:00
Heng Li c6d5dea314 replace with newer versions 2017-06-22 12:30:45 -04:00
Heng Li fbfd4a3eff to replace 2017-06-22 12:30:22 -04:00
Heng Li 8e0d73740e moved aln-dp.tex to ksw2/tex (a new repo) 2017-06-18 11:21:34 -04:00
Heng Li fe8327500f implemented SSE version; NOT working yet 
need to take a rest. Debugging is going to be tough.
 2017-06-16 21:35:51 -04:00
Heng Li 359b829350 fixed a boundary bug in global() 
Actually global2() is correct. It is global() that is wrong.
 2017-06-16 12:47:09 -04:00
Heng Li 7d33acbccc diagonal global almost working 
one shot, though gaps not left-aligned at the boundary
 2017-06-16 12:17:23 -04:00
Heng Li c4564c31a2 explain DP 2017-06-15 19:37:48 -04:00
Heng Li 78fe89d1ab revert to fixed band 2017-06-14 14:22:23 -04:00
Heng Li d3f17b1e05 updated ksw 2017-06-11 16:51:01 -04:00
Heng Li 372698bb23 disable k-mer intersection for now 
My current focus is long-read mapping. This functionality is not needed right now.
 2017-06-11 14:13:41 -04:00
Heng Li b04e4b9215 r36: bring back primary; don't output all mappings 2017-06-08 15:28:19 -04:00
Heng Li 6c099bef89 removed some debugging code 
not necessary when we can print PAF
 2017-06-07 14:49:11 -04:00
Heng Li 19e43571c1 r34: removed a bit unused code 2017-06-07 14:35:57 -04:00
Heng Li be9a7f4e41 removed the old print code 2017-06-07 14:24:31 -04:00
Heng Li 8ad5cfde42 output PAF 2017-06-07 14:18:32 -04:00
Heng Li c01f2dd757 fixed a bug 2017-06-07 11:40:13 -04:00
Heng Li 77c76c1e14 fixed an integer overflow 2017-06-06 22:20:45 -04:00
Heng Li c1c946aa67 fixed memory leaks 
though some of them are not really leaks when kalloc is in use.
 2017-06-06 21:45:55 -04:00
Heng Li e6adb673f9 fixed a stupid bug 2017-06-06 15:45:42 -04:00
Heng Li a2958a4836 minor tweaks 2017-06-06 15:31:21 -04:00
Heng Li d816e48fce fixed a bug in chaining 2017-06-06 14:33:43 -04:00
Heng Li 6d4348db44 dp chaining mostly works, but fails sometimes 
which means there are bugs that need to be fixed
 2017-06-06 14:19:50 -04:00
Heng Li 1a9fc04cf0 backup 2017-06-06 10:16:33 -04:00
Heng Li acc7382a30 backup 2017-06-04 16:09:45 -04:00
Heng Li 949d9be872 chaining with DP 2017-05-09 22:20:57 +08:00
Heng Li 2827c29b48 minor backup 2017-05-04 23:22:11 +08:00
Heng Li 10db6b0434 wrong HPC 2017-05-04 17:45:19 +08:00
Heng Li 06adabd0dc clean bill from valgrind 2017-05-04 12:44:49 +08:00
Heng Li 7b53f7aa84 chaining 2017-05-03 20:47:29 +08:00
Heng Li f2ae8eb670 mostly debugging code 2017-05-01 16:50:09 +08:00
Heng Li 2c9f1bce3e k-mer thinning apparently working 2017-04-28 18:24:45 +08:00
Heng Li 7b7fabef4d added idx_stat 2017-04-26 22:52:28 +08:00
Heng Li de367a340c compilable again 2017-04-26 19:36:46 +08:00
Heng Li 56723ad580 moved sum_len out of the index 
as it can be inferred.
 2017-04-19 11:06:24 -04:00
Heng Li f35e152e99 fixed a few memory leaks 2017-04-13 23:05:19 -04:00
Heng Li 9947c953cf sort positions in each bucket 2017-04-12 13:31:12 -04:00
Heng Li 1bf3ae6752 backup 2017-04-09 15:09:39 -04:00
Heng Li 79c9478f46 backup 2017-04-09 14:59:39 -04:00
Heng Li 49b8d23695 indexing not segfault 2017-04-09 14:17:37 -04:00