Heng Li
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30abcf3cf9
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r907: copy tag "cs" in sam2paf
Resolves #310
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2019-01-13 17:52:31 -05:00 |
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Heng Li
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c404f49569
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Release minimap2-2.15 (r905)
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2019-01-10 12:34:45 -05:00 |
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Heng Li
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5b2fdfff9c
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r895: option in asmgene to count autosomal only
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2018-12-14 10:36:47 -05:00 |
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Heng Li
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eef1cee9b7
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r893: added paftools.js vcfpair
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2018-12-01 18:53:03 -05:00 |
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Heng Li
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62bbadf668
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r887: fixed a bug in asmgene
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2018-11-11 21:35:19 -05:00 |
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Heng Li
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cdaf46665a
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r885: compute dup with asmstat
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2018-11-07 00:26:05 -05:00 |
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Heng Li
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59f23f7579
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Release minimap2-2.14 (r883)
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2018-11-06 00:03:16 -05:00 |
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Heng Li
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09e089c3dc
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r872: choose the longest isoform
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2018-11-04 23:48:50 -05:00 |
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Heng Li
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e46cbb7d84
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r871: print erroneous genes
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2018-11-04 20:37:06 -05:00 |
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Heng Li
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57ec73ec6c
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r870: separate <50% and <10%
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2018-11-04 19:31:25 -05:00 |
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Heng Li
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9e27575387
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r869: classify incomplete genes
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2018-11-04 19:21:55 -05:00 |
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Heng Li
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b4ad8d8bf0
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added asmgene
improvements coming; not made public yet
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2018-11-04 17:24:05 -05:00 |
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Heng Li
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e315b9fada
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hidden options to control bp calculation
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2018-11-04 16:36:04 -05:00 |
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Heng Li
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5d5d392c02
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Release minimap2-2.13 (r850)
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2018-10-11 13:18:31 -04:00 |
Torsten Seemann
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34be359e25
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Add -s sample option for VCF output
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2018-09-19 18:24:47 -04:00 |
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Heng Li
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5cfa621b2d
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use unmapped records
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2018-07-07 12:49:15 -05:00 |
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Heng Li
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bcf92b3c46
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compute query coverage
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2018-07-06 21:52:01 -05:00 |
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Heng Li
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097378ab90
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reworked break point counting
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2018-07-06 09:46:26 -04:00 |
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Heng Li
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10bbbe28c5
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added asmstat
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2018-07-05 13:22:32 -04:00 |
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Heng Li
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50dae10421
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paftools call to show statistics on longer indels
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2018-07-03 14:28:09 -04:00 |
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Heng Li
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39f836eac8
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r767: don't crash when there is no "cg" (#153)
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2018-04-24 12:32:37 -04:00 |
apregier
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2e2e69107c
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Small bugfix for paftools.js
The bug resulted in the wrong coverage being printed in some cases.
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2018-04-04 16:29:54 -04:00 |
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Heng Li
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0bf97a367b
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r755: junceval to only evaluate chromosomes
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2018-03-24 23:10:06 -04:00 |
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Heng Li
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1c504d72e4
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r754: option to only change name
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2018-03-23 12:27:11 -04:00 |
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Heng Li
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242ff4e91d
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r745: junceval - recognize "-" as file name
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2018-03-15 12:51:46 -04:00 |
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Heng Li
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77ebd479f4
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r743: added VCF output to "call"
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2018-03-12 21:51:31 -04:00 |
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Heng Li
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ccaf12e1a2
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r734: removed debugging print in call()
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2018-03-09 23:46:21 -05:00 |
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Heng Li
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70428ca3a8
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speedup tag parsing for sam2paf
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2018-03-02 10:17:55 -05:00 |
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Heng Li
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9aea79d621
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faster tag parsing
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2018-03-02 10:09:14 -05:00 |
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Heng Li
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1770988627
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make calling work with sam2paf output
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2018-03-02 10:03:06 -05:00 |
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Heng Li
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2bfdad34bb
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minor cleanup to last commit
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2018-03-02 01:07:37 -05:00 |
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Heng Li
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953766cedd
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generate cs; not carefully tested
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2018-03-02 00:14:55 -05:00 |
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Heng Li
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dc61301d9f
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sam2paf cleanup
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2018-03-01 21:58:12 -05:00 |
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Heng Li
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e1f18690f6
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paftools-r713: fixed bug for cov1 regions
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2018-02-16 12:20:46 -05:00 |
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Heng Li
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3b17d62ccd
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minor doc improvements
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2018-02-12 22:27:02 -05:00 |
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Heng Li
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874b8c4795
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rework misc/README; progressing but unfinished
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2018-02-12 22:06:05 -05:00 |
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Heng Li
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f66de7df59
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updated paftools revision number to r702
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2018-02-12 11:39:04 -05:00 |
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Heng Li
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fbbd4e0968
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changed output messages for clarity
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2018-02-12 11:32:32 -05:00 |
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Heng Li
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8c89ba005e
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merged cnt-feat into paftools
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2018-02-12 11:29:42 -05:00 |
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Heng Li
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50775a1e6f
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added liftOver
tested on a few toy examples
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2018-02-12 11:12:23 -05:00 |
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Heng Li
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87cf650168
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r697: fixed wrong #mapped reads in junceval
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2018-02-09 18:45:57 -05:00 |
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Heng Li
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42dab6319b
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don't call SNPs involving 'n'
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2018-02-09 13:27:17 -05:00 |
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Heng Li
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8428809369
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convert MUMmer's delta to PAF
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2018-02-09 12:14:28 -05:00 |
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Heng Li
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642af5591e
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merged intron-eval into paftools
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2018-02-09 11:07:14 -05:00 |
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Heng Li
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2025a6279a
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merged gff2bed and mapstat to paftools
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2018-02-09 10:47:12 -05:00 |
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Heng Li
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3465b04724
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merged a few converters to paftools
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2018-02-09 10:23:30 -05:00 |
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Heng Li
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66c5e71fa8
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merging scripts into one long script
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2018-02-09 10:00:35 -05:00 |
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Heng Li
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dbf284b2d9
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r684: separate end score from min_chain_score
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2018-02-05 11:40:38 -05:00 |
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Heng Li
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3df5015668
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General doc improvements
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2018-02-02 21:45:46 -05:00 |
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Heng Li
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756379bf83
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Documented paf2diff.js (more to come later)
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2018-02-02 14:43:58 -05:00 |