Heng Li
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6db9b7579c
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Better MSVC support
* get rid of alloca()
* no variable-sized arrays
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2017-09-03 11:05:55 -04:00 |
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Heng Li
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2b8681ead7
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fixed memory leak in example
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2017-09-02 17:55:25 -04:00 |
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Heng Li
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0a3ebdc916
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for better windows compatibility
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2017-09-02 17:52:33 -04:00 |
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Heng Li
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b97620afed
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moved gettimeofday() to misc.c
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2017-09-02 17:40:10 -04:00 |
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Heng Li
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743d26eab0
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Merge pull request #20 from nanoporetech/msvc14
ONT source code changes to compile with MSVC 14
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2017-09-02 14:35:02 -07:00 |
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Heng Li
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62535ecd7f
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Merge branch 'dev'
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2017-09-01 10:06:21 -07:00 |
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Heng Li
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40665d1083
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Merge pull request #23 from simonrharris/segfaultfix
Fixed segfault caused when reading from index file
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2017-09-02 00:46:55 +08:00 |
Simon Harris
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4db1c0295c
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Fixed segfault caused when reading from index file
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2017-09-01 15:48:59 +01:00 |
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Heng Li
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d4074874ee
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r316: get rid of a harmless gcc warning
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2017-09-01 20:25:27 +08:00 |
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Heng Li
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eccdb3a1ca
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r315: added getopt from musl
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2017-09-01 20:20:34 +08:00 |
Stefan von Deylen
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a3c3db6b9b
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ONT source code changes to compile with MSVC 14
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2017-08-30 16:25:20 +01:00 |
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Heng Li
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2641613686
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various minor improvements
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2017-08-25 17:56:16 +08:00 |
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Heng Li
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5f96d851a8
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added spliced alignment example
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2017-08-25 14:11:54 +08:00 |
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Heng Li
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bf8246f872
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Release minimap2-2.1-r311
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2017-08-25 13:35:55 +08:00 |
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Heng Li
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5cbd776651
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test data for spliced alignment
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2017-08-25 13:17:56 +08:00 |
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Heng Li
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0fe1a224ab
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r309: improved SAM header output
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2017-08-25 10:35:58 +08:00 |
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Heng Li
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240f6caaff
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backup manuscript
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2017-08-24 22:05:14 +08:00 |
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Heng Li
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b8bdac7e64
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backup
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2017-08-22 17:45:01 +08:00 |
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Heng Li
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19e4b2aab0
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backup
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2017-08-20 22:10:03 +08:00 |
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Heng Li
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ce859dbe1c
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evaluate introns
this simplies the metrics
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2017-08-20 21:54:59 +08:00 |
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Heng Li
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a4c41f64a5
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the final version
to be replaced by intron-eval
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2017-08-20 21:54:35 +08:00 |
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Heng Li
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5ed2faf270
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minor tuning to the matching rules
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2017-08-19 16:21:49 +08:00 |
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Heng Li
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8058c85b72
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moved appendix to methods; detailed splice aln
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2017-08-18 23:33:57 +08:00 |
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Heng Li
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993a2bb521
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r301: separate introns from deletions
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
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2017-08-18 15:31:15 +08:00 |
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Heng Li
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64c1389e1a
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Merge branch 'master' into splice
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2017-08-17 23:39:27 +08:00 |
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Heng Li
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81cff97208
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r299: support -h: output to stdout; return 0
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2017-08-17 23:38:31 +08:00 |
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Heng Li
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bbb37d95f2
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support inserting RG lines
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2017-08-17 23:34:09 +08:00 |
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Heng Li
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2cde8d257c
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r297: bidirectional RNA alignment
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2017-08-17 06:02:44 -04:00 |
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Heng Li
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b5f5929bf9
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r296: expose splicing related options to CLI
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2017-08-13 21:37:51 -04:00 |
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Heng Li
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28f86688ab
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r295: gap closure from the middle of non-HPC k
This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
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2017-08-12 23:48:43 -04:00 |
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Heng Li
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43506edbc5
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backup: preliminary boundary alignment
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2017-08-12 23:10:14 -04:00 |
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Heng Li
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bcfe00d2ad
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minor formatting changes
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2017-08-12 19:09:33 -04:00 |
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Heng Li
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17c19e5819
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exts2 working
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2017-08-12 19:06:59 -04:00 |
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Heng Li
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61eef0575c
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separate out spliced alignment; not right yet
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2017-08-12 18:54:32 -04:00 |
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Heng Li
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53b3265d84
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r290: in techrep, explain spliced alignment
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2017-08-12 15:40:49 -04:00 |
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Heng Li
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a23df2dc91
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r289: changed CLI help only
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2017-08-12 12:40:07 -04:00 |
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Heng Li
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5a74088b74
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r288: changed max intron length to 200k
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2017-08-12 12:39:21 -04:00 |
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Heng Li
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d240318741
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r287: refined CLI options and manpage
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2017-08-12 12:26:04 -04:00 |
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Heng Li
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0f4c823b0c
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r286: ignore introns when computing max seg score
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2017-08-12 10:58:16 -04:00 |
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Heng Li
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2d11aaa830
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option to print all exons for debugging
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2017-08-12 10:04:16 -04:00 |
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Heng Li
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30b8cb4672
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option to print correct exons
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2017-08-11 17:50:21 -04:00 |
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Heng Li
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0c1760bc86
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bugfix; print errors; better rules
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2017-08-11 16:28:52 -04:00 |
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Heng Li
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a99358bc3d
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r282: reduced intron cost; added eval script
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2017-08-11 00:06:01 -04:00 |
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Heng Li
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163fa36ee6
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r281: don't open long gaps on query
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2017-08-10 15:04:59 -04:00 |
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Heng Li
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c59b0781bc
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r280: output introns as "N" in the cdna mode
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2017-08-09 11:45:02 -04:00 |
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Heng Li
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7429b12164
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Merge branch 'master' into cdna
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2017-08-08 22:00:24 -04:00 |
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Heng Li
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9e1125edda
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r277: abort if query/-d missing (#11)
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2017-08-08 21:46:15 -04:00 |
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Heng Li
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4db0d1034b
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Show travis CI status
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2017-08-08 21:32:56 -04:00 |
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Heng Li
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3dbe23b34e
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Merge branch 'dev'
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2017-08-08 21:30:32 -04:00 |
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Heng Li
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6840370f3c
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Release minimap2-2.0 (r275)
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2017-08-08 21:16:25 -04:00 |