Heng Li
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68d99f0edb
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Merge branch 'cs-tag' into dev
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2017-08-04 14:31:46 -04:00 |
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Heng Li
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fd66ab5413
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blast-like output working
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2017-08-04 14:31:21 -04:00 |
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Heng Li
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71f82759af
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convert paf to maf
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2017-08-04 13:05:46 -04:00 |
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Heng Li
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648cdd8a3b
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minor wording changes
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2017-08-04 10:21:10 -04:00 |
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Heng Li
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7e231cfd3a
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minor wording improvement
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2017-08-03 21:28:01 -04:00 |
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Heng Li
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95d3c30ae3
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rephrasing a bit to avoid the apparent TeX bug
Several hours sank into this. Damned...
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2017-08-03 20:19:00 -04:00 |
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Heng Li
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f57fd8c790
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added one transition phrase
as there are no subsubsections now
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2017-08-03 18:01:48 -04:00 |
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Heng Li
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c70b20ee6d
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removed subsubsection
TeX Live 2016 doesn't work with section and content on the same line.
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2017-08-03 17:58:36 -04:00 |
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Heng Li
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e8d00a8c8c
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removed trailing ^M
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2017-08-03 17:20:43 -04:00 |
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Heng Li
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ed4efd77bc
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minor modifications
I will submit this version arXiv. There is definitely room for improvement, but
as a semi-formal technical report, it should be good for now.
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2017-08-03 12:47:36 -04:00 |
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Heng Li
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295874ea30
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spell check
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2017-08-03 12:17:58 -04:00 |
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Heng Li
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9ec5f51afb
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the first draft
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2017-08-03 12:12:55 -04:00 |
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Heng Li
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28ab4d1f72
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backup
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2017-08-02 22:59:58 -04:00 |
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Heng Li
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6c9390b54a
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backup
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2017-08-02 19:52:31 -04:00 |
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Heng Li
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9306299e4d
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added benchmark results
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2017-08-01 15:12:49 -04:00 |
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Heng Li
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0c563e1868
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Merge branch 'dev' into tex
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2017-08-01 13:53:16 -04:00 |
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Heng Li
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8b1e36c609
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minor tweaks to the evaluation script
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2017-08-01 13:52:29 -04:00 |
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Heng Li
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d933a263d7
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backup
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2017-08-01 13:29:02 -04:00 |
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Heng Li
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7542b4b40a
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Makefile for TeX
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2017-08-01 10:42:33 -04:00 |
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Heng Li
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d6181de844
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added tech notes
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2017-08-01 10:38:33 -04:00 |
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Heng Li
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12cea727b8
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r238: bugfix to cs - rev sequence not complemented
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2017-08-01 10:33:21 -04:00 |
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Heng Li
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cd105b47f2
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r237: fixed a bug in outputting cs:Z
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2017-07-31 14:49:39 -04:00 |
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Heng Li
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35f232c3fa
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r236: in cs tag, output differences in lowercase
for easy eyeballing
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2017-07-31 12:17:48 -04:00 |
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Heng Li
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4c0713ee14
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r235: optionally output tag cs in PAF
cs encodes the query, the reference sequence and CIGAR.
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2017-07-31 12:06:49 -04:00 |
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Heng Li
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46de0fbdad
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Merge pull request #8 from rikuu/master
fix self-comparison in index parameter override check
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2017-07-30 15:10:29 -04:00 |
Riku Walve
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9e09c1ae72
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fix self-comparison in index parameter override check
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2017-07-30 21:46:25 +03:00 |
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Heng Li
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d8d4d29b68
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Release minimap2-2.0rc1-r232
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2017-07-30 14:32:40 -04:00 |
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Heng Li
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e51dfd0330
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added NEWS
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2017-07-30 14:20:03 -04:00 |
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Heng Li
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1f78e1ee53
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r230: code formatting changes only
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2017-07-30 12:31:40 -04:00 |
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Heng Li
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5934d68772
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r229: a new way to prevent out-of-band backtrack
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2017-07-29 23:52:30 -04:00 |
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Heng Li
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fa99d28d34
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r228: reduced unnecessary INV alignment
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2017-07-29 20:21:53 -04:00 |
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Heng Li
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d08b7a0c51
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r227: use local alignment for INV alignment
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2017-07-29 17:40:53 -04:00 |
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Heng Li
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da3db3c095
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r226: only try inv alignment for primary
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2017-07-29 14:09:35 -04:00 |
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Heng Li
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783ead6f47
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r225: removed a debugging line
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2017-07-29 13:21:38 -04:00 |
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Heng Li
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19d6ec885e
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r224: inversion alignment around Z-drop break
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2017-07-29 13:09:10 -04:00 |
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Heng Li
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120bebc290
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ake
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2017-07-29 11:01:49 -04:00 |
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Heng Li
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5e3eecd6d4
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r222: no effective changes
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2017-07-29 10:31:46 -04:00 |
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Heng Li
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2179e9e24b
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r221: output SA in the SAM output
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2017-07-28 23:08:39 -04:00 |
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Heng Li
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84922cfe41
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clarify that wrong seeding mainly occurs in LCRs
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2017-07-28 14:33:15 -04:00 |
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Heng Li
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ebbe9c1eb8
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r219: fixed a bug caused by skipping tandem seeds
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2017-07-28 14:06:56 -04:00 |
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Heng Li
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c672690564
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r218: increase the frequency of SW slightly
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2017-07-28 13:30:42 -04:00 |
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Heng Li
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f4fee60188
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r217: ignore tandem seeds during alignment
This helps a tiny bit.
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2017-07-28 12:26:56 -04:00 |
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Heng Li
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254280b8af
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r216: a bit cleanup; identical output to r215
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2017-07-28 11:54:18 -04:00 |
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Heng Li
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fc965805f7
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r215: bring back a log gap component
Otherwise chaining may more often break a long gap into several gaps.
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2017-07-28 00:17:19 -04:00 |
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Heng Li
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667b32a516
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added algorithm overview
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2017-07-27 18:50:39 -04:00 |
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Heng Li
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2c79580649
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r213: more careful solution to wrong seeds
a little better, but not good enough!
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2017-07-27 13:19:11 -04:00 |
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Heng Li
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b927838495
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r212: better heuristic to fix wrong seeding
but not good enough. Will explore more.
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2017-07-27 11:24:51 -04:00 |
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Heng Li
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371e20cc7c
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r211: a better heurstic to reduce false seeds
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2017-07-26 23:56:38 -04:00 |
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Heng Li
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8b08a2ec41
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added first-only and all-primary modes to eval
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2017-07-26 19:32:26 -04:00 |
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Heng Li
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9f728dd96a
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tunable overlap ratio
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2017-07-26 18:30:29 -04:00 |