Heng Li
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a03d01f944
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r878: XA is given to the best alignment
Non-ALT hits may get ALT hits in the XA tag. This will simplify haplotype
assignment.
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2014-09-30 13:50:51 -04:00 |
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Heng Li
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039ea20639
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Merge branch 'dev'
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2014-09-27 23:22:18 -04:00 |
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Heng Li
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0a2cf98293
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r876: optionally ignore idxbase.alt file
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2014-09-27 23:21:50 -04:00 |
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Heng Li
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dae4ca3ced
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r875: invalid SAM output for ALT hits
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2014-09-26 15:29:08 -04:00 |
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Heng Li
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8d61316cc8
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more comments
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2014-09-23 10:33:15 -04:00 |
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Heng Li
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e8e5bbc071
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Merge branch 'dev'
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2014-09-19 23:56:19 -04:00 |
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Heng Li
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5fc0f44e27
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mapQ is not quite right
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2014-09-19 23:39:59 -04:00 |
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Heng Li
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a33ca20499
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separate postalt to a separate script
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2014-09-19 23:23:54 -04:00 |
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Heng Li
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fd42d30910
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Merge branch 'dev'
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2014-09-19 17:05:59 -04:00 |
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Heng Li
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23bc50e240
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removed altlift; suppress primary hit by default
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2014-09-19 17:05:27 -04:00 |
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Heng Li
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7426a750ec
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r868: use soft clip for ALT hits
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2014-09-19 16:58:18 -04:00 |
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Heng Li
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9af36064e8
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r867: fixed a few bugs; added ALT hits to XA
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2014-09-19 16:50:21 -04:00 |
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Heng Li
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7cbcbc4abf
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Merge branch 'dev'
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2014-09-18 11:54:41 -04:00 |
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Heng Li
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b22bed2b5e
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removed <> from markdown
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2014-09-18 11:54:23 -04:00 |
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Heng Li
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954ee5eda9
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Merge branch 'dev'
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2014-09-18 11:52:03 -04:00 |
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Heng Li
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030825ae85
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updated release notes
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2014-09-18 11:51:52 -04:00 |
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Heng Li
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ba7ed47d40
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error in altpost
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2014-09-18 11:18:10 -04:00 |
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Heng Li
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70e9ed0ea9
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Merge branch 'dev'
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2014-09-18 10:50:07 -04:00 |
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Heng Li
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a41afe4c97
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These files were committed on a wrong branch
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2014-09-18 10:49:35 -04:00 |
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Heng Li
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dd1c6619d7
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r858: bugfix in PE alt alignments
Alignments found with mate rescue are not flagged with "is_alt"
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2014-09-18 10:47:21 -04:00 |
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Heng Li
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b9026ecafd
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Merge branch 'dev'
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2014-09-17 23:18:09 -04:00 |
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Heng Li
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a32d44d8d6
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r855: show ALT hits in the PE mode, too
In the previous version, it does not
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2014-09-17 23:07:56 -04:00 |
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Heng Li
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c982443210
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r854: improved the calculation of pa
and build pa filtering into BWA-MEM
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2014-09-17 16:26:28 -04:00 |
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Heng Li
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d677a4325b
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Merge branch 'dev'
Conflicts:
main.c
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2014-09-17 14:22:20 -04:00 |
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Heng Li
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f5a0e576e6
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added postalt to bwa-helper for post processing
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2014-09-17 14:18:40 -04:00 |
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Heng Li
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825ae92e58
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r849: the pa tag now gives a number
... which is the ratio of this hit to the best ALT hit.
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2014-09-17 13:05:35 -04:00 |
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Heng Li
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6f37c14f26
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r848: tag alignments with primary ALT
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2014-09-16 18:52:49 -04:00 |
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Heng Li
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945d39fb79
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Merge branch 'dev'
Conflicts:
main.c
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2014-09-16 14:39:33 -04:00 |
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Heng Li
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a458442b24
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r845: updated NEWS
I will use the new version for a while and then release it.
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2014-09-16 14:38:41 -04:00 |
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Heng Li
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92bc6849a3
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r844: added intra-species contig mapping mode
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2014-09-16 10:53:07 -04:00 |
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Heng Li
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90518f11e3
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r843: presetting for ONT 2d reads
Somewhat working for 1d reads, but not very well
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2014-09-16 10:38:15 -04:00 |
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Heng Li
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152d25ff87
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Merge branch 'dev'
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2014-09-16 10:17:53 -04:00 |
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Heng Li
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230cd16712
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updated dependency
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2014-09-16 10:17:30 -04:00 |
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Heng Li
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d0af3648d1
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Fixed a typo
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2014-09-16 10:16:45 -04:00 |
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Heng Li
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1bdd791539
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r837: removed BAM support
This is not necessary.
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2014-09-16 09:57:35 -04:00 |
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Heng Li
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7244d66833
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r836: a dangerous merge
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2014-09-16 00:37:58 -04:00 |
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Heng Li
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df09f38ad3
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Merge branch 'dev'
Conflicts:
README.md
bwamem.c
bwamem_pair.c
fastmap.c
main.c
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2014-09-16 00:24:41 -04:00 |
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Heng Li
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43ce69104d
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Removed PacBio read-to-read instruction
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2014-09-15 23:59:35 -04:00 |
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Heng Li
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d013ea94b0
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Removed instruction on ALT alignment
Favoring the new method
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2014-09-15 23:45:17 -04:00 |
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Heng Li
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4b6eeb34c8
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r830: optionally fixed chunk size
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2014-09-15 23:42:24 -04:00 |
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Heng Li
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624687b072
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r829: killed a harmless gcc warning
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2014-09-15 23:33:22 -04:00 |
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Heng Li
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5d26ab0ee3
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r828: changed the default scoring for pacbio
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2014-09-15 23:22:05 -04:00 |
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Heng Li
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41b137d202
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Merge pull request #32 from mmoisse/patch-1
Update example Illumina paired-end reads
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2014-09-15 22:59:22 -04:00 |
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Heng Li
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b07587f806
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r827: an alt hit as good as a pri hit as supp
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2014-09-15 16:07:51 -04:00 |
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Heng Li
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bd85af08ab
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r826: improved alt mapping for PE
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2014-09-15 12:13:04 -04:00 |
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Heng Li
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aee53f1334
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r824: ALT mapping seems working
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2014-09-15 00:29:05 -04:00 |
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Heng Li
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015ab3f6c3
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r823: towards ALT support
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2014-09-14 16:41:14 -04:00 |
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Heng Li
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8116bcc786
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Merge branch 'dev' into alt
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2014-09-14 15:40:52 -04:00 |
mmoisse
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dfd8c9eeb6
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Update README.md
The 'Illumina paired-end reads no longer than ~70bp' example should use sampe instead of samse
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2014-09-14 11:26:39 +02:00 |
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Heng Li
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8d2b93156b
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r821: more relax on containing seeds
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2014-09-12 10:35:49 -04:00 |