Heng Li
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de54c9dac2
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r77: fixed an index loading bug (offset not set)
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2017-06-26 13:56:25 -04:00 |
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Heng Li
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10644f2165
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r76: missing header file
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2017-06-26 12:36:37 -04:00 |
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Heng Li
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4b8e88a5f4
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use long options
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2017-06-26 12:31:36 -04:00 |
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Heng Li
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640b1a1727
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command-line option to control CIGAR output
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2017-06-26 11:41:09 -04:00 |
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Heng Li
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24d7f7f8b1
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disabled dynamic banding; buggy
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2017-06-25 22:43:15 -04:00 |
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Heng Li
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b1077ff14c
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sam output
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2017-06-25 22:05:20 -04:00 |
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Heng Li
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39083be9ab
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separated formating printing
for SAM in future; and for performance
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2017-06-25 16:13:54 -04:00 |
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Heng Li
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7780ab792a
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removed some comment lines
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2017-06-25 11:53:35 -04:00 |
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Heng Li
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56364200c8
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avoid contained hits due to split
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2017-06-25 11:43:50 -04:00 |
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Heng Li
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f20d550a59
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fixed the NM bug
due to reversed CIGAR
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2017-06-25 11:24:39 -04:00 |
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Heng Li
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b261a4a74b
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zdrop sort of works, but has issues
left and right extensions are different; NM is also wrong
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2017-06-25 10:52:14 -04:00 |
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Heng Li
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72dfb0c99e
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fixed a bug in ksw2
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2017-06-25 10:22:13 -04:00 |
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Heng Li
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ef5dd318ca
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implemented chain splitting; NOT tested!!!
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2017-06-24 22:57:43 -04:00 |
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Heng Li
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aa5881e7bb
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backup
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2017-06-24 22:51:31 -04:00 |
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Heng Li
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d08b58d21f
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minor
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2017-06-24 19:33:59 -04:00 |
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Heng Li
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672782f03a
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simplified hp_len a little
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2017-06-24 19:27:58 -04:00 |
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Heng Li
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2d8fda9586
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an alternative strategy to fix for HPC
it makes the result better, but still not quite right.
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2017-06-24 09:26:24 -04:00 |
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Heng Li
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6088dc11ff
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wrong SW score
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2017-06-23 23:24:49 -04:00 |
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Heng Li
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0c274280ae
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output the original score
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2017-06-23 22:56:50 -04:00 |
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Heng Li
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2987be288c
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output cigar
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2017-06-23 22:53:47 -04:00 |
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Heng Li
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35b84f88c6
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backup
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2017-06-23 22:42:15 -04:00 |
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Heng Li
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523a8832ad
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backup
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2017-06-23 20:57:17 -04:00 |
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Heng Li
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7ed26a4857
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backup
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2017-06-23 19:31:23 -04:00 |
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Heng Li
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d75b5b4e8a
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backup; NOT working yet
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2017-06-23 19:21:47 -04:00 |
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Heng Li
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4fea3d778a
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backup
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2017-06-23 18:57:00 -04:00 |
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Heng Li
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6c8368c24c
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get the left-extension sequence correctly
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2017-06-23 18:25:47 -04:00 |
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Heng Li
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990f7b0b71
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backup
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2017-06-23 15:13:53 -04:00 |
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Heng Li
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4ae0b46972
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min_ksw_len
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2017-06-23 14:38:28 -04:00 |
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Heng Li
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9cd313eae1
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sequence retrieval working
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2017-06-23 14:11:56 -04:00 |
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Heng Li
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326d91deb0
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backup
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2017-06-23 14:06:00 -04:00 |
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Heng Li
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44cdd18de0
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start to work on alignment
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2017-06-23 13:44:45 -04:00 |
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Heng Li
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c6d5dea314
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replace with newer versions
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2017-06-22 12:30:45 -04:00 |
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Heng Li
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fbfd4a3eff
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to replace
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2017-06-22 12:30:22 -04:00 |
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Heng Li
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8e0d73740e
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moved aln-dp.tex to ksw2/tex (a new repo)
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2017-06-18 11:21:34 -04:00 |
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Heng Li
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fe8327500f
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implemented SSE version; NOT working yet
need to take a rest. Debugging is going to be tough.
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2017-06-16 21:35:51 -04:00 |
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Heng Li
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359b829350
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fixed a boundary bug in global()
Actually global2() is correct. It is global() that is wrong.
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2017-06-16 12:47:09 -04:00 |
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Heng Li
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7d33acbccc
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diagonal global almost working
one shot, though gaps not left-aligned at the boundary
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2017-06-16 12:17:23 -04:00 |
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Heng Li
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c4564c31a2
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explain DP
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2017-06-15 19:37:48 -04:00 |
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Heng Li
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78fe89d1ab
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revert to fixed band
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2017-06-14 14:22:23 -04:00 |
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Heng Li
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d3f17b1e05
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updated ksw
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2017-06-11 16:51:01 -04:00 |
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Heng Li
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372698bb23
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disable k-mer intersection for now
My current focus is long-read mapping. This functionality is not needed right now.
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2017-06-11 14:13:41 -04:00 |
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Heng Li
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b04e4b9215
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r36: bring back primary; don't output all mappings
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2017-06-08 15:28:19 -04:00 |
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Heng Li
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6c099bef89
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removed some debugging code
not necessary when we can print PAF
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2017-06-07 14:49:11 -04:00 |
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Heng Li
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19e43571c1
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r34: removed a bit unused code
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2017-06-07 14:35:57 -04:00 |
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Heng Li
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be9a7f4e41
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removed the old print code
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2017-06-07 14:24:31 -04:00 |
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Heng Li
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8ad5cfde42
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output PAF
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2017-06-07 14:18:32 -04:00 |
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Heng Li
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c01f2dd757
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fixed a bug
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2017-06-07 11:40:13 -04:00 |
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Heng Li
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77c76c1e14
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fixed an integer overflow
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2017-06-06 22:20:45 -04:00 |
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Heng Li
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c1c946aa67
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fixed memory leaks
though some of them are not really leaks when kalloc is in use.
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2017-06-06 21:45:55 -04:00 |
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Heng Li
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e6adb673f9
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fixed a stupid bug
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2017-06-06 15:45:42 -04:00 |