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Author SHA1 Message Date
chhylp123 2c18ec30da fix memory leak of print_utg 2023-05-12 11:31:34 -04:00
chhylp123 18b649aadb fixed missing/false duplication for diploid asm 2023-04-17 19:58:00 -04:00
chhylp123 0efcc14499 fix chain spliting bug 2023-04-14 16:43:41 -04:00
chhylp123 84e642d20d fix bubble on-the-fly 2023-04-13 10:16:14 -04:00
chhylp123 7e855ba5e2 update README 2023-04-06 23:16:59 -04:00
chhylp123 5df5892f33 update for rescuing missing contigs 2023-04-06 23:14:41 -04:00
chhylp123 503cd0f7cc 0.19.2->0.19.3 2023-03-22 12:25:39 -04:00
chhylp123 86b7dd424a avoid misassemblies; better polyploidy graph 2023-03-22 12:23:53 -04:00
chhylp123 d4773a497f disable postjoin for the ul assembly 2023-03-13 15:43:22 -04:00
chhylp123 f67faa9c34 path-max and path-min to avoid misassemblies 2023-03-13 11:13:57 -04:00
chhylp123 3407c7029e coverage adjustment for polyploidy 2023-03-12 17:02:29 -04:00
chhylp123 2218bac8aa clean output 2023-03-10 23:42:29 -05:00
chhylp123 b533067835 enable dbg-ovec 2023-03-10 23:30:24 -05:00
chhylp123 384b721d84 clean output 2023-03-10 15:46:23 -05:00
chhylp123 8b79a3f22e disable function for tangles with low-coverage ul 2023-03-10 15:34:10 -05:00
chhylp123 af4be8ca1a disable integer correction; disable contain dedup 2023-03-10 09:12:07 -05:00
chhylp123 85c643e85d clean contained read; fixed for deep_graph_clean 2023-03-07 15:28:24 -05:00
chhylp123 a0f2f70d91 better resolution for complex regions 2023-02-27 09:35:50 -05:00
chhylp123 04f660fd8c bug fixed for mask calculation 2023-02-24 00:36:52 -05:00
chhylp123 2b4b4f29e0 r525 2023-02-21 20:22:56 -05:00
chhylp123 8ea2d5a622 r523-phasing-across chains 2023-02-21 15:44:45 -05:00
chhylp123 7d5c793109 additional cluster for phasing 2023-02-20 23:38:27 -05:00
chhylp123 3abd3793fb clean graph alignment 2023-02-20 14:50:55 -05:00
chhylp123 b55e4396d2 prt_dbg_gfa -> before transitive reduction 2023-02-17 11:00:15 -05:00
chhylp123 fc598d71f6 0.18.6 -> 0.18.7 2023-02-16 12:16:24 -05:00
chhylp123 286b897881 r513 2023-02-16 00:04:06 -05:00
chhylp123 f2da12a2ad 508 —> futhur graph cleaning 2023-02-12 22:49:12 -05:00
chhylp123 1166b92eb4 r502->additional alignment 2023-01-25 09:39:41 -05:00
chhylp123 78ef43ce8e r500 2023-01-23 15:28:43 -05:00
chhylp123 dc07898f68 Merge branch 'hifiasm_dev_debug' of https://github.com/chhylp123/hifiasm into hifiasm_dev_debug 2023-01-23 15:25:37 -05:00
chhylp123 db2edc0ffb fix exit(1) for bin_only 2023-01-23 15:25:01 -05:00
chhylp123 8ff5a1370d Merge pull request #348 from chhylp123/master 
auto merge
 2023-01-17 10:27:58 -05:00
chhylp123 f054b11e0e Merge pull request #382 from chhylp123/hifiasm_dev_debug 
Hifiasm dev debug
 2023-01-17 04:53:24 -05:00
chhylp123 25d6857d44 r499->false duplications 2023-01-17 04:49:56 -05:00
chhylp123 46391eba26 fix bubble popping bugs 2023-01-15 22:29:20 -05:00
chhylp123 2969af129d Merge pull request #380 from chhylp123/hifiasm_dev_debug 
Hifiasm dev debug
 2023-01-12 01:23:04 -05:00
chhylp123 2bf5119bb5 update help information 2023-01-12 01:22:34 -05:00
chhylp123 197cd4d77e 0.18.3 -> 0.18.4 2023-01-12 00:22:23 -05:00
chhylp123 7ad498f631 r495-reuse misjoin detection 2023-01-12 00:21:43 -05:00
chhylp123 0613b18af9 r493 ->HiC/UL/Trans 2023-01-11 20:38:45 -05:00
chhylp123 34948a093c Merge pull request #368 from chhylp123/hifiasm_dev_debug 
fixed het/hom node bugs
 2022-12-08 03:07:43 -05:00
chhylp123 a674110b23 fixed het/hom node bugs 2022-12-08 03:07:14 -05:00
chhylp123 6743dcf204 Merge pull request #363 from chhylp123/hifiasm_dev_debug 
cleaner assembly graph
 2022-12-06 09:52:47 -05:00
chhylp123 a3b72457f0 cleaner assembly graph 2022-12-06 09:52:00 -05:00
chhylp123 5b928dfe1d Merge pull request #361 from chhylp123/hifiasm_dev_debug 
r465
 2022-12-02 09:41:42 -05:00
chhylp123 786f8bdff0 r465 2022-12-02 09:40:25 -05:00
chhylp123 2400236f7c Merge pull request #358 from chhylp123/hifiasm_dev_debug 
slightly better assembly graph
 2022-11-28 14:47:35 -05:00
chhylp123 a4d6cebc32 slightly better assembly graph 2022-11-28 14:42:48 -05:00
chhylp123 25dcaaabec Merge pull request #356 from chhylp123/hifiasm_dev_debug 
Hifiasm dev debug
 2022-11-25 20:51:04 -05:00
chhylp123 9a454576e1 fixed memory issue within gen_single_khit 2022-11-25 20:49:14 -05:00
chhylp123 6de08fd91f debug assert 2022-11-25 15:20:32 -05:00
chhylp123 deb31948e1 Merge pull request #354 from chhylp123/hifiasm_dev_debug 
fixed gap filling with UL
 2022-11-25 11:49:27 -05:00
chhylp123 fc76af1285 fixed gap filling with UL 2022-11-25 11:46:37 -05:00
chhylp123 b84e7ec328 Merge pull request #351 from chhylp123/hifiasm_dev_debug 
0.17.4-r455
 2022-11-17 18:06:11 -05:00
chhylp123 979d83f68d 0.17.4-r455 2022-11-17 18:05:35 -05:00
chhylp123 f9c5e09388 Merge pull request #350 from chhylp123/hifiasm_dev_debug 
r454
 2022-11-17 18:04:35 -05:00
chhylp123 9747c42123 r454 2022-11-17 18:02:52 -05:00
chhylp123 b4b53b8efd Merge pull request #349 from chhylp123/hifiasm_dev_debug 
bugs for bubble/hom assembly
 2022-11-17 18:01:50 -05:00
chhylp123 553a8745cc bugs for bubble/hom assembly 2022-11-17 18:01:08 -05:00
chhylp123 a1867ec9a2 Merge pull request #347 from chhylp123/hifiasm_dev_debug 
update README
 2022-11-17 12:29:12 -05:00
chhylp123 1afecdcecc update README 2022-11-17 12:26:33 -05:00
chhylp123 66ad203018 Merge pull request #346 from chhylp123/hifiasm_dev_debug 
fix utg el bug
 2022-11-17 12:19:28 -05:00
chhylp123 152bae2dfb fix utg el bug 2022-11-17 12:18:40 -05:00
chhylp123 22c44befa5 Merge pull request #345 from chhylp123/hifiasm_dev_debug 
merge UL
 2022-11-17 09:33:40 -05:00
chhylp123 9831afaf26 code clean 2022-11-17 09:31:56 -05:00
chhylp123 2c7b164f11 tmp cache 2022-11-10 19:37:52 -05:00
chhylp123 46acc8a2f6 version with wrong realignment 2022-11-07 02:35:26 -05:00
chhylp123 612c1ab712 cuttoff before debugging 2022-11-05 09:03:23 -04:00
chhylp123 e66c003b65 cleaner graph 2022-11-01 21:44:13 -04:00
chhylp123 f4b6223fde cutoff-r426-avoid-tip 2022-10-31 15:18:52 -04:00
chhylp123 3d1787e57a ul_refine_alignment 2022-10-29 17:15:19 -04:00
chhylp123 249bee7304 done contain clean 2022-10-27 17:05:46 -04:00
chhylp123 df3e0eeaa3 read extract 2022-10-19 13:23:25 -04:00
chhylp123 3d65bef9de adjusted chain sc 2022-10-09 18:14:07 -04:00
chhylp123 1d0562ebd1 done second alignment 2022-10-09 16:59:54 -04:00
chhylp123 2443e63ef5 done chaining 2022-10-08 14:51:03 -04:00
chhylp123 f92cef38f2 uodate gchain 2022-10-07 15:14:08 -04:00
chhylp123 8a4d6a5f24 done alignemnt 2022-10-04 15:31:23 -04:00
chhylp123 68a74fb16d cigar collect 2022-10-02 14:38:49 -04:00
chhylp123 41437764f0 before window filling 2022-10-01 23:42:38 -04:00
chhylp123 bbd3394b4a lack final alignment 2022-10-01 19:53:02 -04:00
chhylp123 20a7dac82a backup for minimizer 2022-09-28 11:16:09 -04:00
chhylp123 236bc7b9ee backup for minimizer 2022-09-28 11:15:29 -04:00
chhylp123 4c873f9a66 large extension 2022-09-24 22:39:07 -04:00
chhylp123 a297105258 cal_exz_infi 2022-09-24 16:16:54 -04:00
chhylp123 38e00d2086 shared seeds 2022-09-23 22:17:38 -04:00
chhylp123 f4cc895fa0 update ed 2022-09-20 22:48:59 -04:00
chhylp123 4e7bb7eeb9 fix cigar 2022-09-18 23:17:58 -04:00
chhylp123 774c585562 infi ed 2022-09-16 21:34:36 -04:00
chhylp123 54b733ef2f inner define 2022-09-14 21:10:31 -04:00
chhylp123 69d0e18fe5 ed macro 2022-09-14 15:38:55 -04:00
chhylp123 2300dc63bb extension 2022-09-14 00:23:44 -04:00
chhylp123 5da05f308f extend ed alignment 2022-09-13 17:29:27 -04:00
chhylp123 ee51a6dddc seperate alignment 2022-09-04 00:18:51 -04:00
chhylp123 cc16626dfa debug cigar_offset 2022-09-01 23:16:08 -04:00
chhylp123 7b89478b2e code clean 2022-08-28 02:39:05 -04:00
chhylp123 8b7ca5f0c3 revised HiFi phasing 2022-08-23 10:36:35 -04:00
chhylp123 54465dd9ac tangle resolved 2022-08-16 23:35:56 -04:00
chhylp123 89e0d1aafa UL graph with graph cleaning 2022-08-02 15:48:16 -04:00
chhylp123 91de382bde before contain keeping 2022-07-27 10:41:57 -04:00