 Heng Li
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1f7d3f46c9
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removed clang
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2021-05-10 22:23:22 -04:00 |
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Heng Li
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d4cc3551e8
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added code of conduct
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2021-05-10 21:49:48 -04:00 |
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Heng Li
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8187f177ec
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Merge branch 'master' of github.com:chhylp123/hifiasm
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2021-05-10 21:48:31 -04:00 |
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Heng Li
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c9b61dcd78
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added CI
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2021-05-10 21:48:18 -04:00 |
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Heng Li
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dfd7720f5a
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clarify that hifiasm doesn't do scaffolding
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2021-04-17 16:28:12 -04:00 |
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Heng Li
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325bcebf9c
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Merge branch 'doc-update'
I will not create another PR for this...
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2021-04-17 16:07:49 -04:00 |
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Heng Li
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a0e4cbf80a
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minor changes
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2021-04-17 16:07:34 -04:00 |
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Heng Li
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2464297370
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Merge pull request #101 from chhylp123/doc-update
Updated README
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2021-04-17 16:03:48 -04:00 |
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Heng Li
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d9c47e21db
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updated README
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2021-04-17 16:01:32 -04:00 |
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Heng Li
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863b20773a
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Merge branch 'master' into dev-lh3
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2021-03-18 16:11:43 -04:00 |
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Heng Li
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8e98fb2276
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Merge branch 'master' into dev-lh3
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2021-03-02 19:27:44 -05:00 |
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Heng Li
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88f6261f7a
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Merge pull request #73 from molecules/patch-1
Added citation
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2021-02-09 00:39:13 -05:00 |
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Heng Li
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205eadf346
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r334: ignore a high-occ seed in a small window
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2021-01-23 16:25:52 -05:00 |
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Heng Li
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61befd357a
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r333: also subsample high-freq mz during indexing
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2021-01-22 23:17:25 -05:00 |
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Heng Li
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3b8f73fbab
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r332: increased mz sample dist from 200 to 500
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2021-01-22 10:31:29 -05:00 |
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Heng Li
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8ff87685e5
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updated Makefile dependencies
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2021-01-21 11:58:50 -05:00 |
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Heng Li
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da672118e5
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r330: unimap heuristic for mz sampling
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2021-01-21 11:05:37 -05:00 |
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Heng Li
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02f0b5dd22
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r329: a bit code cleanup
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2020-11-03 00:44:15 -05:00 |
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Heng Li
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dcb583bd69
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r328: use binomial heap for general cases
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2020-11-01 22:49:06 -05:00 |
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Heng Li
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6fa4d44426
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r327: choose up to 3 high-freq minimizers
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2020-11-01 10:44:02 -05:00 |
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Heng Li
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f02eb66e6a
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r326: select high-occ k-mers (experimental)
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2020-10-29 22:36:54 -04:00 |
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Heng Li
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f37c4e29fa
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a bit refactoring for the next change
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2020-10-29 18:24:47 -04:00 |
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Heng Li
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ef8c047559
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removed unused ha_sketch
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2020-10-29 11:28:43 -04:00 |
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Heng Li
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eddb8173da
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added --min-hist-cnt for #49
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2020-10-26 16:28:30 -04:00 |
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Heng Li
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8cb131dca3
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added a "Why hifiasm?" section
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2020-10-05 01:01:58 -04:00 |
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Heng Li
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00128c3076
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Fixed the wrong download link
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2020-10-04 23:01:16 -04:00 |
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Heng Li
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519d5b1eb1
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Updated the download link
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2020-10-04 23:00:27 -04:00 |
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Heng Li
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ebedae2a21
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updated Makefile
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2020-08-05 17:33:14 -04:00 |
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Heng Li
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94008c02ac
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Re-release hifiasm-0.9 (r289)
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2020-07-19 14:44:28 -04:00 |
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Heng Li
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1e4d67ee64
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r288: reorganized command line help messages
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2020-07-19 13:43:30 -04:00 |
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Heng Li
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ff4ef89fe3
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r287: fixed the INT32_MAX compiling error
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2020-07-19 11:22:23 -04:00 |
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Heng Li
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309e885365
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Release hifiasm-0.8 (r279)
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2020-06-27 19:56:49 -04:00 |
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Heng Li
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5cb42cafc2
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more README changees
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2020-06-27 19:25:38 -04:00 |
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Heng Li
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f1e78720aa
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more getting started; added NA12878 and links
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2020-06-27 14:22:39 -04:00 |
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Heng Li
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97f6efc4da
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r255: faster way to extract reads
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2020-06-03 21:38:59 -04:00 |
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Heng Li
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eddbc61952
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r254: added --ex-list and --ex-iter
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2020-06-03 20:46:34 -04:00 |
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Heng Li
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e247c5f042
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r253: Merge branch 'master' into dev-lh3
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2020-05-23 21:43:22 -04:00 |
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Heng Li
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f6ea45b58a
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r251: always keep the best hits
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2020-05-08 00:40:53 -04:00 |
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Heng Li
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e544360043
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r250: fixed a bug in selecting top chains
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2020-05-07 14:49:49 -04:00 |
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Heng Li
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3364a29b87
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r249: make max overlap error rate CLI options
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2020-05-06 01:16:50 -04:00 |
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Heng Li
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331e437c72
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r248: contained reads not handled properly
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2020-05-03 00:27:53 -04:00 |
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Heng Li
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85c57fd087
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r246: made purge_dups optional for trio binning
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2020-04-15 23:57:18 -04:00 |
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Heng Li
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a06ee39433
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r244: use 3 rounds of error correction by default
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2020-04-13 19:51:15 -04:00 |
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Heng Li
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8907e9c64f
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r243: Merge branch 'master' into dev-lh3
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2020-04-13 15:18:21 -04:00 |
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Heng Li
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946a0f4115
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r238: got rid of LIS chaining
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2020-04-13 14:44:10 -04:00 |
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Heng Li
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b333addb6c
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r237: fall back to DP chaining more often
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2020-04-13 08:39:05 -04:00 |
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Heng Li
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cc166c8ff5
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r235: clarified option -f
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2020-04-12 19:42:02 -04:00 |
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Heng Li
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cdd5f3e4e0
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r234: fixed a bug for -r of an odder number
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2020-04-12 19:25:53 -04:00 |
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Heng Li
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2d985569f1
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Merge branch 'master' into dev-lh3
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2020-04-12 18:57:42 -04:00 |
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Heng Li
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2c4de3a326
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r230: the first anchor score was not adjusted
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2020-04-12 10:39:42 -04:00 |
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Heng Li
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75a89c214d
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r229: LIS score is still not exactly right
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2020-04-12 10:19:28 -04:00 |
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Heng Li
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22b681b830
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r228: resolved a compiler warning
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2020-04-12 09:56:50 -04:00 |
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Heng Li
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4d7600361c
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r226b: prefer unique anchors
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2020-04-11 22:28:21 -04:00 |
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Heng Li
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c4397a9400
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r226: more careful about ma_hit_t_alloc memory
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2020-04-11 22:05:07 -04:00 |
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Heng Li
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e6b5b666a2
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r224: versioning
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2020-04-11 00:14:33 -04:00 |
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Heng Li
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54fa1a9aed
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Merge branch 'master' into dev-lh3
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2020-04-11 00:08:35 -04:00 |
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Heng Li
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c710c6ea48
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r221: sync with hifiasm parameter
Probably has no practical effect
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2020-04-10 21:49:01 -04:00 |
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Heng Li
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c37ea00d6a
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r220: resumed versioning
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2020-04-10 19:12:32 -04:00 |
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Heng Li
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ad1b79a6bb
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Merge branch 'flt-p' into dev-lh3
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2020-04-10 14:03:44 -04:00 |
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Heng Li
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22b2e1e9e1
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r217: fixed a bug in LIS chaining score
Also fall back to DP chaining more often
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2020-04-10 13:25:25 -04:00 |
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Heng Li
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15591c9038
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improve documentation
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2020-04-10 11:04:35 -04:00 |
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Heng Li
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71328f7423
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r215: binning with external list (NOT TESTED!!)
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2020-04-10 01:06:43 -04:00 |
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Heng Li
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f32bfc904a
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r215: prepare for list-based binning
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2020-04-10 00:12:19 -04:00 |
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Heng Li
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7a35bd7fcc
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r213: renamed trio binning output files
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2020-04-09 20:40:01 -04:00 |
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Heng Li
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c3f032da37
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r212: LIS chaining was not working
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2020-04-09 10:43:37 -04:00 |
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Heng Li
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c41aae0630
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r211: added --write-paf/--write-ec/--skip-triobin
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2020-04-08 22:32:54 -04:00 |
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Heng Li
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23dbfdef77
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Merge branch 'master' into dev-lh3
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2020-04-08 18:32:33 -04:00 |
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Heng Li
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8efcdefcaf
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r207: multiple input files were not working
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2020-04-07 12:40:10 -04:00 |
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Heng Li
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a79fd0f360
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r206: apply trio binning when loading from binary
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2020-04-06 16:58:29 -04:00 |
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Heng Li
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1bbca54d8d
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r205: resume versioning
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2020-04-06 09:59:43 -04:00 |
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Heng Li
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2d0087104f
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Merge branch 'master' into merge3
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2020-04-06 08:25:54 -04:00 |
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Heng Li
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7f580850e8
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Merge branch 'master' of github.com:chhylp123/hifiasm
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2020-04-06 08:25:21 -04:00 |
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Heng Li
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adbc65feda
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r201: automatically adjust -N
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2020-04-05 22:43:01 -04:00 |
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Heng Li
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3773610532
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r200: reworked multi-thread for better efficiency
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2020-04-05 16:18:14 -04:00 |
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Heng Li
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46f83e152d
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r199: renamed pre.ovlp.bin to pre.ec.bin
Also updated the Makefile dependencies
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2020-04-05 13:45:50 -04:00 |
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Heng Li
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0f1994fc1f
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r198: made VERBOSE_GFA a CL option --dbg-gfa
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2020-04-05 13:01:03 -04:00 |
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Heng Li
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31356f9e02
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r197: added an assertion test/suppressed warnings
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2020-04-05 12:22:28 -04:00 |
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Heng Li
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16a3d58dc9
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r196: fixed a compiling error
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2020-04-05 12:14:20 -04:00 |
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Heng Li
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5917aa2f36
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Merge branch 'chain-tune' into merge2
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2020-04-05 12:07:13 -04:00 |
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Heng Li
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f0c53e9948
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r192: estimate buffer memory
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2020-04-05 11:17:12 -04:00 |
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Heng Li
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8c27dbb52f
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r191: changed the default to -N400 -k51 -w51
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2020-04-04 12:55:19 -04:00 |
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Heng Li
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4e3c15ec83
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r190: fixed an if_exact() bug
caused by reverse complement again
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2020-04-04 00:51:38 -04:00 |
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Heng Li
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dbe66d259d
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r189: print statistics
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2020-04-04 00:14:53 -04:00 |
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Heng Li
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69c32066d4
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r188: reduced duplicated code
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2020-04-03 23:53:43 -04:00 |
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Heng Li
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18b69f1a72
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r187: reversed round in clear_opt()
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2020-04-03 22:19:55 -04:00 |
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Heng Li
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76de054331
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r186: fixed memory leaks when loading from disk
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2020-04-03 20:35:47 -04:00 |
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Heng Li
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992322f8e3
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r185: fixed a few more memory leaks
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2020-04-03 20:14:20 -04:00 |
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Heng Li
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6f4d0debe4
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r184: fixed a memory leak in POA
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2020-04-03 14:10:40 -04:00 |
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Heng Li
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d529dcea3f
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r183: reorganized the major workflow
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2020-04-03 13:34:07 -04:00 |
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Heng Li
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ffba3ce0ef
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r182: explain -N
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2020-04-03 10:42:09 -04:00 |
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Heng Li
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968b4caef9
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r181: limit the max number of chains
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2020-04-02 21:55:00 -04:00 |
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Heng Li
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3838482851
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moved sorting to anchor.cpp for future changes
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2020-04-02 19:18:29 -04:00 |
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Heng Li
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483ceb852c
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r179: replace one qsort() with ks_introsort()
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2020-04-02 10:34:43 -04:00 |
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Heng Li
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7776dee103
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r178: speedup chaining
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2020-04-02 09:30:23 -04:00 |
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Heng Li
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878fe943c3
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r177: combine the hifiasm and minimap2 heuristics
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2020-04-01 23:07:42 -04:00 |
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Heng Li
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b7e5d1c4d3
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r176: enabled the minimap2 chaining heuristic
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2020-04-01 22:06:14 -04:00 |
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Heng Li
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e75b93ae12
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r175: start versioning
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2020-03-28 11:52:14 -04:00 |
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Heng Li
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1d4f34a36c
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changed the default -D from 7 to 5
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2020-03-28 11:43:44 -04:00 |
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Heng Li
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4fa3cbfd46
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double the chunk size
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2020-03-27 22:46:51 -04:00 |
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Heng Li
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5e16483b43
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option to skip k-mer filtering
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2020-03-27 22:32:39 -04:00 |
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