Heng Li
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41fd8a966a
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Documented ov-eval.js
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2018-02-02 14:18:18 -05:00 |
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Heng Li
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86e4933b1a
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Added TOC
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2018-02-02 14:12:30 -05:00 |
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Heng Li
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a633a744b6
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more doc in misc
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2018-02-02 14:07:17 -05:00 |
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Heng Li
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ddc31f57ba
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Documented some k8 scripts; more coming
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2018-02-02 13:57:08 -05:00 |
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Heng Li
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35d3e064bf
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r677: reduce the change of missing hits
that are close to end of alignments. It is still possible to create examples
that fail the heuristic.
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2018-02-02 10:35:33 -05:00 |
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Heng Li
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997ab9bb2e
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Fixed the description of --dual
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2018-02-01 15:11:51 -05:00 |
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Heng Li
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53ce317e59
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Release minimap2-2.8 (r672)
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2018-02-01 12:50:20 -05:00 |
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Heng Li
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da6947cfa3
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r671: cleanup command line options
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2018-01-31 13:59:52 -05:00 |
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Heng Li
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46d6349af4
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r670: added PE support to mappy
and minor code cleanup
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2018-01-31 11:33:08 -05:00 |
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Heng Li
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12a5a5fa3c
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r669: improved self chain extension (#10)
This has not fully resolved #10, only alleviated the issue.
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2018-01-30 20:05:02 -05:00 |
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Heng Li
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ad18fa490d
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fixed typos
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2018-01-30 10:11:50 -05:00 |
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Heng Li
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43bfa6199d
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r667: warn if one query file has fewer records #92
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2018-01-28 17:36:21 -05:00 |
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Heng Li
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72b9b0e3b6
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r666: report if >=3 query files in SR mode #92
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2018-01-28 17:15:57 -05:00 |
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Heng Li
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6205fa6f21
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document --heap-sort
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2018-01-26 15:15:40 -05:00 |
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Heng Li
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d676a5314b
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r664: use --heat-sort for sr by default
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2018-01-26 12:25:42 -05:00 |
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Heng Li
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dfc78b39d3
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refactor the old sorting
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2018-01-26 09:37:48 -05:00 |
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Heng Li
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7b57c9a619
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heap sort working on MT
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2018-01-26 09:21:45 -05:00 |
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Heng Li
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123bc1d91d
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put option operations in another file
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2018-01-26 08:38:37 -05:00 |
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Heng Li
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dd18307e66
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code backup
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2018-01-25 21:52:49 -05:00 |
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Heng Li
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543fa12e68
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r659: for C++ compatibility
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2018-01-19 10:40:18 -05:00 |
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Heng Li
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af1a871270
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r658: gives a warning if -N0 is used
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2018-01-19 08:33:20 -05:00 |
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Heng Li
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2b71181a37
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r657: check -p (#96)
Well, in principle, every option should be checked. Will do when someone raise
issues...
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2018-01-19 01:03:38 -05:00 |
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Heng Li
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0454e6be91
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explain -M in the manpage
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2018-01-18 11:47:11 -05:00 |
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Heng Li
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33f8157961
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r655: options to map to one strand of the ref #91
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2018-01-16 10:34:30 -05:00 |
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Heng Li
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eecc06086f
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Released minimap2-2.7 (r654)
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2018-01-09 13:16:00 -05:00 |
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Heng Li
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dfea113f28
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r653: the last change may write "N" wrongly
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2018-01-08 11:33:53 -05:00 |
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Heng Li
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1842d7f5b5
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allow to exclude regions
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2018-01-07 22:35:56 -05:00 |
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Heng Li
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f5cfd439ee
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r651: incorrectly treat introns as deletions
This happened when the last operation during backtracking is an intron.
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2018-01-07 19:42:50 -05:00 |
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Heng Li
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248b43cc47
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work with targets in BED12
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2018-01-07 19:39:25 -05:00 |
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Heng Li
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bf72969ab1
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added a bed counter
I know there are tools for this purpose, but they don't quite meet my exact
need.
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2018-01-07 15:19:18 -05:00 |
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Heng Li
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7b5a601d48
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support paired-end reads
this gives unnecessary warnings, which will be fixed later.
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2018-01-07 13:53:26 -05:00 |
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Heng Li
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405d531100
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don't test python v3.3
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2018-01-05 22:17:00 -05:00 |
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Heng Li
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e9607fcd9b
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allow to convert read names
ONT read names are just too long and too hard to compress
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2018-01-05 22:05:15 -05:00 |
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Heng Li
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a465a920ec
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bug in block starts; added color and short-name
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2018-01-05 21:45:56 -05:00 |
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Heng Li
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b20839be77
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more robust ID conversion
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2018-01-05 17:55:24 -05:00 |
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Heng Li
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209beb9955
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convert EnsEMBL to UCSC name (optional)
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2018-01-05 17:41:18 -05:00 |
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Heng Li
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cfe87f50c1
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convert GTF/GFF3 to BED12
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2018-01-05 17:10:43 -05:00 |
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Heng Li
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680b971bb0
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deleted duplicated entries
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2018-01-01 19:52:21 -05:00 |
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Heng Li
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6b0d3c1fa8
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added PHONY and comments to makefile
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2017-12-30 20:54:11 -05:00 |
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Heng Li
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dc9e3dcf4a
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r639: changed -O/-E validation
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2017-12-30 20:39:29 -05:00 |
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Heng Li
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cc75c12905
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r638: disabled scoring checking
I haven't figured out the exact bounds...
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2017-12-30 07:50:40 -05:00 |
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Heng Li
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f159e1c2d3
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new section on HPC k-mers
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2017-12-24 19:11:23 -05:00 |
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Heng Li
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3a375d3436
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renamed paf2ovlp to ov-eval
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2017-12-24 18:04:00 -05:00 |
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Heng Li
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626f10e0d0
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evaluate sensitivity in the same script
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2017-12-24 17:55:42 -05:00 |
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Heng Li
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b997578078
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find reads overlaps based on reference alignment
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2017-12-24 17:20:27 -05:00 |
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Heng Li
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ce8a48d715
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fixed two minor typos in references
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2017-12-24 13:14:47 -05:00 |
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Heng Li
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99879e9e75
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a new section on estimating sequence divergence
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2017-12-24 12:57:38 -05:00 |
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Heng Li
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c969d1a1ce
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updated direct RNA-seq results; cite syndip
and a few minor changes
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2017-12-24 11:06:17 -05:00 |
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Heng Li
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fcac296c4a
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clarify ARM-NEON support in README
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2017-12-18 23:01:44 -05:00 |
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Heng Li
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e420b17496
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r629: API to construct index from strings
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2017-12-18 22:29:46 -05:00 |