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• e401f88e57 update test datasets chhylp123 2020-06-27 13:03:46 -04:00
• 7a2e02cb77 fix typo chhylp123 2020-06-27 12:56:02 -04:00
• 3a88079a6e update typo chhylp123 2020-06-27 12:44:12 -04:00
• be26acc0e0 update readme chhylp123 2020-06-27 12:43:14 -04:00
• 03c9028848 update readme chhylp123 2020-06-27 12:36:33 -04:00
• 0071251c82 update README chhylp123 2020-06-27 12:35:47 -04:00
• 39cf3f5dd8 update README chhylp123 2020-06-27 12:34:41 -04:00
• acba806ce1 update readme chhylp123 2020-06-27 12:30:57 -04:00
• 46987e792a update readme chhylp123 2020-06-27 12:29:23 -04:00
• 1ec650e3e5 update readme chhylp123 2020-06-27 12:27:16 -04:00
• 61657f4b29 update readme chhylp123 2020-06-27 12:06:59 -04:00
• 35ee94f040 update README chhylp123 2020-06-27 11:46:48 -04:00
• ed137c2ac6 update readme chhylp123 2020-06-27 11:38:08 -04:00
• 9cc97472d9 update readme chhylp123 2020-06-27 11:25:21 -04:00
• 449950cddb update readme chhylp123 2020-06-27 10:57:22 -04:00
• 71f6c93d58 add options chhylp123 2020-06-08 17:51:36 -04:00
• 36bfb02298 r257: dropped contained unitigs contain Heng Li 2020-06-08 15:43:21 -04:00
• afa93e4bbb prepare for further changes Heng Li 2020-06-06 21:55:41 -04:00
• 97f6efc4da r255: faster way to extract reads Heng Li 2020-06-03 21:38:59 -04:00
• eddbc61952 r254: added --ex-list and --ex-iter Heng Li 2020-06-03 20:46:34 -04:00
• e247c5f042 r253: Merge branch 'master' into dev-lh3 Heng Li 2020-05-23 21:43:22 -04:00
• d36e1e7782 fixed bugs for trio-binning v0.7 chhylp123 2020-05-17 11:53:12 -04:00
• f6ea45b58a r251: always keep the best hits Heng Li 2020-05-08 00:40:53 -04:00
• e544360043 r250: fixed a bug in selecting top chains Heng Li 2020-05-07 14:49:49 -04:00
• 3364a29b87 r249: make max overlap error rate CLI options Heng Li 2020-05-06 01:16:50 -04:00
• 331e437c72 r248: contained reads not handled properly Heng Li 2020-05-03 00:27:53 -04:00
• 7f6725ead3 expose purge_dups v0.6 chhylp123 2020-04-18 00:45:47 -04:00
• 85c57fd087 r246: made purge_dups optional for trio binning Heng Li 2020-04-15 23:57:18 -04:00
• 57e979ca17 update for v0.5.0 v0.5 chhylp123 2020-04-14 00:10:58 -04:00
• a06ee39433 r244: use 3 rounds of error correction by default Heng Li 2020-04-13 19:51:15 -04:00
• 8907e9c64f r243: Merge branch 'master' into dev-lh3 Heng Li 2020-04-13 15:18:21 -04:00
• 946a0f4115 r238: got rid of LIS chaining Heng Li 2020-04-13 14:44:10 -04:00
• b333addb6c r237: fall back to DP chaining more often Heng Li 2020-04-13 08:39:05 -04:00
• 4216384df6 update README v0.4 chhylp123 2020-04-12 20:59:49 -04:00
• 3120db1340 update README chhylp123 2020-04-12 20:53:18 -04:00
• 69e8282b9a update README chhylp123 2020-04-12 20:51:18 -04:00
• b93baa3cbd update README chhylp123 2020-04-12 20:46:54 -04:00
• cc166c8ff5 r235: clarified option -f Heng Li 2020-04-12 19:42:02 -04:00
• cdd5f3e4e0 r234: fixed a bug for -r of an odder number Heng Li 2020-04-12 19:25:53 -04:00
• 2d985569f1 Merge branch 'master' into dev-lh3 Heng Li 2020-04-12 18:57:42 -04:00
• 57b16e9e1f fix warning chhylp123 2020-04-12 17:46:30 -04:00
• b245e9a760 fix warning chhylp123 2020-04-12 17:46:20 -04:00
• 2c4de3a326 r230: the first anchor score was not adjusted Heng Li 2020-04-12 10:39:42 -04:00
• 75a89c214d r229: LIS score is still not exactly right Heng Li 2020-04-12 10:19:28 -04:00
• 22b681b830 r228: resolved a compiler warning Heng Li 2020-04-12 09:56:50 -04:00
• 4d7600361c r226b: prefer unique anchors Heng Li 2020-04-11 22:28:21 -04:00
• c4397a9400 r226: more careful about ma_hit_t_alloc memory Heng Li 2020-04-11 22:05:07 -04:00
• e6b5b666a2 r224: versioning Heng Li 2020-04-11 00:14:33 -04:00
• 54fa1a9aed Merge branch 'master' into dev-lh3 Heng Li 2020-04-11 00:08:35 -04:00
• 20c6c1d2e6 update trio-binning chhylp123 2020-04-10 23:32:15 -04:00
• c710c6ea48 r221: sync with hifiasm parameter Heng Li 2020-04-10 21:49:01 -04:00
• c37ea00d6a r220: resumed versioning Heng Li 2020-04-10 19:12:32 -04:00
• ad1b79a6bb Merge branch 'flt-p' into dev-lh3 Heng Li 2020-04-10 14:03:44 -04:00
• 943b6947cb update purge_dup by LIS flt-p chhylp123 2020-04-10 13:58:36 -04:00
• 22b2e1e9e1 r217: fixed a bug in LIS chaining score Heng Li 2020-04-10 13:25:25 -04:00
• 15591c9038 improve documentation Heng Li 2020-04-10 11:04:35 -04:00
• 71328f7423 r215: binning with external list (NOT TESTED!!) Heng Li 2020-04-10 01:06:43 -04:00
• f32bfc904a r215: prepare for list-based binning Heng Li 2020-04-10 00:12:19 -04:00
• 7a35bd7fcc r213: renamed trio binning output files Heng Li 2020-04-09 20:40:01 -04:00
• c3f032da37 r212: LIS chaining was not working Heng Li 2020-04-09 10:43:37 -04:00
• c41aae0630 r211: added --write-paf/--write-ec/--skip-triobin Heng Li 2020-04-08 22:32:54 -04:00
• 23dbfdef77 Merge branch 'master' into dev-lh3 Heng Li 2020-04-08 18:32:33 -04:00
• a288415111 bug fixing for purge_dup chhylp123 2020-04-08 16:55:04 -04:00
• 8efcdefcaf r207: multiple input files were not working Heng Li 2020-04-07 12:40:10 -04:00
• 9cc563c7c6 do hap alignment in parallel chhylp123 2020-04-07 11:18:28 -04:00
• a79fd0f360 r206: apply trio binning when loading from binary Heng Li 2020-04-06 16:58:29 -04:00
• 1bbca54d8d r205: resume versioning Heng Li 2020-04-06 09:59:43 -04:00
• 2d0087104f Merge branch 'master' into merge3 Heng Li 2020-04-06 08:25:54 -04:00
• 7f580850e8 Merge branch 'master' of github.com:chhylp123/hifiasm Heng Li 2020-04-06 08:25:21 -04:00
• 87fc103e63 fix small bug chhylp123 2020-04-06 02:03:34 -04:00
• adbc65feda r201: automatically adjust -N Heng Li 2020-04-05 22:43:01 -04:00
• 3773610532 r200: reworked multi-thread for better efficiency Heng Li 2020-04-05 16:18:14 -04:00
• 46f83e152d r199: renamed pre.ovlp.bin to pre.ec.bin Heng Li 2020-04-05 13:45:50 -04:00
• 0f1994fc1f r198: made VERBOSE_GFA a CL option --dbg-gfa Heng Li 2020-04-05 13:01:03 -04:00
• 31356f9e02 r197: added an assertion test/suppressed warnings Heng Li 2020-04-05 12:22:28 -04:00
• 16a3d58dc9 r196: fixed a compiling error Heng Li 2020-04-05 12:14:20 -04:00
• 5917aa2f36 Merge branch 'chain-tune' into merge2 Heng Li 2020-04-05 12:07:13 -04:00
• c57b63653d Merge pull request #8 from chhylp123/flt-p chhylp123 2020-04-05 11:44:56 -04:00
• f0c53e9948 r192: estimate buffer memory chain-tune Heng Li 2020-04-05 11:17:12 -04:00
• ac3fcc339a for purge_dup chhylp123 2020-04-05 11:10:56 -04:00
• 8c27dbb52f r191: changed the default to -N400 -k51 -w51 Heng Li 2020-04-04 12:55:19 -04:00
• 4e3c15ec83 r190: fixed an if_exact() bug Heng Li 2020-04-04 00:51:38 -04:00
• dbe66d259d r189: print statistics Heng Li 2020-04-04 00:14:53 -04:00
• 69c32066d4 r188: reduced duplicated code Heng Li 2020-04-03 23:53:43 -04:00
• 18b69f1a72 r187: reversed round in clear_opt() Heng Li 2020-04-03 22:19:55 -04:00
• 76de054331 r186: fixed memory leaks when loading from disk Heng Li 2020-04-03 20:35:47 -04:00
• 992322f8e3 r185: fixed a few more memory leaks Heng Li 2020-04-03 20:14:20 -04:00
• 6f4d0debe4 r184: fixed a memory leak in POA Heng Li 2020-04-03 14:10:40 -04:00
• d529dcea3f r183: reorganized the major workflow Heng Li 2020-04-03 13:34:07 -04:00
• ffba3ce0ef r182: explain -N Heng Li 2020-04-03 10:42:09 -04:00
• 968b4caef9 r181: limit the max number of chains Heng Li 2020-04-02 21:55:00 -04:00
• 3838482851 moved sorting to anchor.cpp for future changes Heng Li 2020-04-02 19:18:29 -04:00
• 483ceb852c r179: replace one qsort() with ks_introsort() Heng Li 2020-04-02 10:34:43 -04:00
• 7776dee103 r178: speedup chaining Heng Li 2020-04-02 09:30:23 -04:00
• 878fe943c3 r177: combine the hifiasm and minimap2 heuristics Heng Li 2020-04-01 23:07:42 -04:00
• b7e5d1c4d3 r176: enabled the minimap2 chaining heuristic Heng Li 2020-04-01 22:06:14 -04:00
• e75b93ae12 r175: start versioning Heng Li 2020-03-28 11:52:14 -04:00
• 1d4f34a36c changed the default -D from 7 to 5 Heng Li 2020-03-28 11:43:44 -04:00
• 4fa3cbfd46 double the chunk size Heng Li 2020-03-27 22:46:51 -04:00
• 5e16483b43 option to skip k-mer filtering Heng Li 2020-03-27 22:32:39 -04:00