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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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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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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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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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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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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76206f574f
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support both SAM and PAF as input
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2017-12-02 21:57:19 -05:00 |
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Heng Li
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e575f884e1
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convert spliced PAF to BED
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2017-12-02 21:23:41 -05:00 |
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Heng Li
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cbdb6c069f
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when there are incorrect anno, warn but not abort
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2017-11-24 12:48:49 -05:00 |
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Heng Li
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39a9666246
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convert PAF to LAST's cigar output
also added the support of BLAST-like output for "--cs=short".
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2017-11-18 20:30:44 -05:00 |
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Heng Li
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662d05dc02
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fixed incorrect var coordinate
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2017-11-12 20:25:33 -05:00 |
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Heng Li
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379457c18b
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use mapq threshold
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2017-11-12 19:01:34 -05:00 |
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Heng Li
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03169d590b
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print cov-1 regions (not BED output any more)
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2017-11-12 18:45:49 -05:00 |
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Heng Li
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8c8d446820
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find regions covered by one contig
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2017-11-12 18:41:01 -05:00 |
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Heng Li
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0ddb064f17
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dnadiff-like script; improvement coming
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2017-11-12 15:07:29 -05:00 |
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Heng Li
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a13691d00d
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eval script works with /[12] in SAM
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2017-09-27 23:33:59 -04:00 |
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Heng Li
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92ec8bd859
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added the /1 or /2 suffix
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2017-09-26 12:04:35 -04:00 |
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Heng Li
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6a82a21dee
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r361: improved mapq for short reads
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2017-09-13 15:32:39 -04:00 |
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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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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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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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5b10667967
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sim-eval.js to support mason2 read names and SAM
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2017-08-07 13:28:33 -04:00 |
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Heng Li
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bd1541dce1
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renamed simulation-related scripts
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2017-08-07 13:26:25 -04:00 |
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Heng Li
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1597f2b030
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convert mason2 SAM to fastq
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2017-08-07 12:45:34 -04:00 |
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Heng Li
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3217178d4a
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fixed k8 download page
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2017-08-04 14:53:00 -04:00 |
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Heng Li
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b40598fa91
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added paf2aln.js example
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2017-08-04 14:51:33 -04:00 |
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Heng Li
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269b8661b9
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minor clarification
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2017-08-04 14:49:25 -04:00 |
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Heng Li
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890d7bbd5b
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added README for misc scripts
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2017-08-04 14:46:31 -04:00 |
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Heng Li
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1aca0d5098
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copied sam2paf.js here for completeness
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2017-08-04 14:44:37 -04:00 |
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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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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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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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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 |