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451 Commits 11 Branches 54 Tags
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Author SHA1 Message Date
chhylp123 26aacdcc2c correct gchains 2021-10-14 15:33:16 -04:00
chhylp123 908b4f3786 bug fix 2021-10-10 14:47:16 -04:00
chhylp123 cb320b88f3 debug ul 2021-10-10 13:37:32 -04:00
chhylp123 7dd4a848b9 debug graph 2021-09-26 13:51:13 -04:00
chhylp123 ed814abf35 before branch 2021-09-16 17:16:30 -04:00
chhylp123 ab80851b94 mempcpy -> memcpy 2021-09-12 17:43:43 -04:00
chhylp123 5e84db0ec9 adjust skew weight 2021-09-10 17:18:48 -04:00
chhylp123 809ca18dda r373 2021-09-10 17:17:44 -04:00
chhylp123 17b5cb21d3 tmp macro 2021-08-30 09:30:48 -04:00
chhylp123 e230b3a55f 0.16.0 release 2021-08-22 21:58:00 -04:00
chhylp123 37b07e4d33 better seeding 2021-08-22 09:53:34 -04:00
chhylp123 bfff640a82 dp opt 2021-08-12 11:16:10 -04:00
chhylp123 6ea66e1290 resolve conflicts 2021-07-27 20:11:22 -04:00
chhylp123 0c81c341d5 update r351 2021-07-27 19:51:20 -04:00
chhylp123 3c8a933b8a Merge remote-tracking branch 'origin/dev-lh3' 2021-07-27 19:50:29 -04:00
chhylp123 f7c3a7c998 fix typo 2021-07-26 00:29:30 -04:00
chhylp123 321acb2d8a update for r350 2021-07-26 00:16:00 -04:00
chhylp123 b14f894160 seperate purgeing and hom peak 2021-07-25 11:23:06 -04:00
chhylp123 6a043540b5 update README 2021-07-22 01:16:28 -04:00
chhylp123 62b7418257 update 0.15.5 2021-07-22 00:59:52 -04:00
chhylp123 a531a4cbda debugging for huge datasets 2021-06-27 07:48:29 -04:00
chhylp123 0410662841 print misjoin debug 2021-06-23 09:49:44 -04:00
chhylp123 5a400af39d r342-misjoin 2021-06-19 14:09:09 -04:00
chhylp123 e3b721c29a r340 2021-06-16 16:44:08 -04:00
chhylp123 5b0a0c85ef ovlp filter 2021-06-13 17:35:09 -04:00
chhylp123 7e06dec2d0 Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly 2021-06-09 20:11:54 -04:00
chhylp123 9dc530cbfb low hamming for sampels with low het rate 2021-06-09 20:10:50 -04:00
chhylp123 ca67e7a9b3 rollback 2021-05-31 18:16:20 -04:00
chhylp123 aa164949f2 backup phasing 2021-05-31 04:19:05 -04:00
chhylp123 e774a83be2 debug mbg 2021-05-30 09:02:25 -04:00
chhylp123 a39f01f4d8 haplotype popping 2021-05-24 19:43:50 -04:00
chhylp123 9e6dde7fb2 backpup 2021-05-22 10:48:49 -04:00
chhylp123 46c0157f79 new ovlp collect 2021-05-22 10:47:58 -04:00
chhylp123 626787ab8a complex cleaning 2021-05-20 17:03:18 -04:00
chhylp123 5c1680e998 fix missed ug when bubble popping 2021-05-19 10:16:23 -04:00
chhylp123 b12e008416 new somatic variant popping 2021-05-19 09:52:40 -04:00
chhylp123 be8e1e3117 sc debug 2021-05-17 00:12:41 -04:00
chhylp123 2bbac713ef init scaffold 2021-05-15 11:45:05 -04:00
chhylp123 4105dd360e correction 2021-05-11 13:01:06 -04:00
chhylp123 7918396d21 collect contig alignment + renew_utg bug fixed 2021-05-09 17:47:50 -04:00
chhylp123 03adce6202 k-mer idx for par 2021-05-06 21:31:40 -04:00
chhylp123 9ea4f6917f resolve centromere 2021-05-06 07:59:51 -04:00
chhylp123 24e5453781 bug fix 2021-05-02 14:16:36 -04:00
chhylp123 9c205c8271 resove tangle by hic 2021-04-30 22:44:48 -04:00
chhylp123 9b31d47379 exit(0) for --help 2021-04-28 23:10:51 -04:00
chhylp123 71e91f3fc2 assgin disconnected parts 2021-04-28 20:27:43 -04:00
chhylp123 2fc2268268 phasing improvement 2021-04-27 21:35:49 -04:00
chhylp123 11430d6a3b r329 2021-04-25 14:50:36 -04:00
chhylp123 1456686665 fast weight 2021-04-25 06:05:23 -04:00
chhylp123 80877b9d0d Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly 2021-04-24 07:00:05 -04:00
chhylp123 e52e897113 clean code 2021-04-24 00:17:08 -04:00
chhylp123 c972c64b39 add "n-weight" 2021-04-24 00:03:36 -04:00
chhylp123 7b07e355b7 bug fix for bubble scanning 2021-04-23 20:40:43 -04:00
chhylp123 a5b29b00bd topo phasing 2021-04-22 22:38:52 -04:00
chhylp123 278efaa876 block phasing 2021-04-21 10:58:58 -04:00
chhylp123 475ebb8075 keep long range information 2021-04-20 01:29:15 -04:00
chhylp123 39c19618e8 backup hic 2021-04-18 21:57:16 -04:00
chhylp123 49ead1ef35 bub disable 2021-04-17 04:23:32 -04:00
chhylp123 4bc43cec92 bug fixed 2021-04-17 00:31:19 -04:00
chhylp123 efacf8e796 bug fixing 2021-04-16 22:26:28 -04:00
chhylp123 f8ee584291 code clean 2021-04-16 20:28:48 -04:00
chhylp123 1e86e3dc02 best flipping 2021-04-14 18:50:20 -04:00
chhylp123 67c7218264 fix distance bug 2021-04-13 01:18:49 -04:00
chhylp123 36afbce9bc update unitig distance 2021-04-12 04:54:06 -04:00
chhylp123 7235f6426f back_up_hic 2021-04-11 10:59:26 -04:00
chhylp123 8f733750c4 variant calling 2021-04-10 21:58:53 -04:00
chhylp123 3218618bb4 keep k_trans 2021-04-08 23:58:12 -04:00
chhylp123 1a6f386823 backup trans_chain 2021-04-04 20:27:19 -04:00
chhylp123 8e75eb5a05 keep l1 trans 2021-04-04 14:00:28 -04:00
chhylp123 ebfc04d253 clean purge_dups 2021-04-03 16:26:58 -04:00
chhylp123 46e899bbae backup r321 2021-04-01 21:02:57 -04:00
chhylp123 0605aa1961 r317 2021-03-27 02:46:48 -04:00
chhylp123 24a19d7976 more accurate purging 2021-03-26 18:07:30 -04:00
chhylp123 d89a630ff3 update contig flipping 2021-03-25 03:03:19 -04:00
chhylp123 9e3e1e8bab update r351 2021-03-20 23:08:55 -04:00
chhylp123 ede6ccef00 fix misassemblies 2021-03-20 18:36:02 -04:00
chhylp123 e6e6dbf7b3 remove unnecessary bin files of Hi-C 2021-03-18 13:44:30 -04:00
chhylp123 2db42c8c00 update version number 2021-03-18 13:18:46 -04:00
chhylp123 98a04c168a update r313 2021-03-18 05:26:33 -04:00
chhylp123 3b4953521f trio bug fixed 2021-03-16 02:36:19 -04:00
chhylp123 8e4b98f0a6 bubble label 2021-03-14 03:25:19 -04:00
chhylp123 4c2ce6fc6b update trans chain 2021-03-10 22:46:50 -05:00
chhylp123 8aa87fdce8 purge_dups for high het 2021-03-08 20:52:11 -05:00
chhylp123 e8b92f7a40 backup for hic 2021-02-18 00:58:25 -05:00
chhylp123 d2ca12604b update r312 2021-02-14 14:17:43 -05:00
chhylp123 d2bf15eba4 update r311 2021-02-14 13:32:02 -05:00
chhylp123 c47a1df4b0 fix chain bug 2021-02-14 12:47:51 -05:00
chhylp123 8855604d99 fix chain bug 2021-02-14 12:45:37 -05:00
chhylp123 dd48e3e15e Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly 2021-02-14 00:00:55 -05:00
chhylp123 02fa015e28 fix memory leak 2021-02-13 23:58:39 -05:00
chhylp123 18086e2c2e update 0.14-r310 2021-02-13 23:21:45 -05:00
chhylp123 5bb22f701c debug hic_hits 2021-02-09 18:40:49 -05:00
chhylp123 8467d58ef1 for v0.14 2021-02-09 13:00:23 -05:00
chhylp123 fda13cb0e4 update -z 2021-02-02 12:45:50 -05:00
chhylp123 02b9a3e109 hic multiple rounds 2021-01-31 18:49:08 -05:00
chhylp123 75ce7cd576 for v0.14-hic 2021-01-31 10:34:21 -05:00
chhylp123 a009026e65 fix bug for broken bubbles 2021-01-15 07:33:13 -05:00
chhylp123 88f5b11f04 bubble graph 2021-01-01 04:50:42 -05:00
chhylp123 c545fd84c7 hic bubble 2020-12-29 09:15:44 -05:00
chhylp123 5d506e82c9 phasing 2020-12-28 03:35:17 -05:00