aaron
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cfebe5c731
|
clean-up the docs a little
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4375 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-29 05:02:41 +00:00 |
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aaron
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702449d835
|
adding a Python script to roll back tribble to the correct version, for users who want to checkout historical versions of the GATK code. This code cross references the current checkout date with the Tribble logs, and pulls the closest (price-is-right style) revision.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4374 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-29 05:01:46 +00:00 |
chartl
|
37613810bf
|
Tired of writing vcf_hg18_to_b36 over and over again when necessary. Added a -r flag to this script that does it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4363 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-28 14:51:57 +00:00 |
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chartl
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40274ba7dc
|
Do this the right way
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4310 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-19 04:30:48 +00:00 |
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chartl
|
fa8cfd3031
|
Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4309 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-19 02:45:16 +00:00 |
depristo
|
b57a0a0310
|
improvements to the report code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-15 00:45:13 +00:00 |
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depristo
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5de1124997
|
more useful reports
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4259 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-12 14:03:44 +00:00 |
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depristo
|
c524a9ec83
|
Minor usability improvements to reporting tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4224 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-08 02:56:25 +00:00 |
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depristo
|
924e16f4f0
|
More robust analysis tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4187 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-01 20:24:04 +00:00 |
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depristo
|
0c54bf4195
|
Better reporting and now with a special mode for listing exceptions
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4183 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-01 16:19:51 +00:00 |
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depristo
|
fc5caa98a5
|
Improved reporting now with metrics by day/week/etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4180 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-01 02:43:13 +00:00 |
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depristo
|
8683087756
|
Suppl. tools for working with and displaying GATK run reports
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4176 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-31 20:32:22 +00:00 |
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depristo
|
9556004dbb
|
now supports -o option as well as verbose output mode
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4162 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-29 16:00:00 +00:00 |
kiran
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7671502e1b
|
Changes from James Pirruccello: now can handle differences between UCSC and NCBI tables, properly sorting despite the contig prefix differences (presence or absence of 'chr'), and converts NCBI format to UCSC format for use by the GenomicAnnotator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4132 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-26 19:02:29 +00:00 |
corin
|
83624e3af3
|
updated to deal with new cleaning pipeline outputs and potentially infinity TI/TV
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4098 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-24 16:01:09 +00:00 |
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depristo
|
669d9096e3
|
now support -o output option, useful for pipelines
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3959 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-06 14:57:04 +00:00 |
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chartl
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6dcb63888d
|
Be smart about the headers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3912 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-30 16:11:16 +00:00 |
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chartl
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eeb767a012
|
Remove legacy "out"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3911 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-30 15:01:02 +00:00 |
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chartl
|
f20cdbe60a
|
Modified to work with MT containing VCFs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3910 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-30 14:59:59 +00:00 |
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chartl
|
52f24c86fa
|
Script to split a provided interval list into contigs. Excesses will be dropped into the last provided file. Works like splitIntervals.sh. This is for Queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3895 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 16:42:53 +00:00 |
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corin
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3596b1529f
|
module for listing out samples for data processing and firehose reporting
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3847 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-21 15:05:41 +00:00 |
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corin
|
1209b165bf
|
Now accepts command line args and prints paths to vcf, bams and beds
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3846 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-21 15:04:58 +00:00 |
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depristo
|
2bdb011865
|
Improvements to 1KG processing pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3807 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-16 15:33:47 +00:00 |
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corin
|
74f705d943
|
fixed silly syntax errors
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3805 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-16 15:08:46 +00:00 |
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corin
|
917469ef43
|
This script produces information for a firehose job-finished email
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3804 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-16 14:44:52 +00:00 |
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chartl
|
19a5830186
|
Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3784 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-13 17:33:15 +00:00 |
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chartl
|
9cc1a411b2
|
Altering the formatting of the annotation to work better with VariantEval's AminoAcidTransition
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3782 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-13 16:31:14 +00:00 |
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chartl
|
80a5ddfa2f
|
Memory string added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3771 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-12 20:43:19 +00:00 |
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chartl
|
46c39f2d53
|
Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3768 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-12 19:13:32 +00:00 |
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depristo
|
dd978dd525
|
misc. changes to python scripts
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3751 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-09 00:13:35 +00:00 |
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depristo
|
cf910d9cc2
|
misc. useful updates to python library
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3683 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-30 16:33:32 +00:00 |
weisburd
|
e7939f7036
|
Fixed error message
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3653 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-28 14:50:28 +00:00 |
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weisburd
|
1cb8f51f8c
|
Fixed -t arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3634 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:44:10 +00:00 |
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weisburd
|
3cd0570c1e
|
Now can run with multiple processes, multiple threads, or both
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3633 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:25:01 +00:00 |
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weisburd
|
dae3ce2c0f
|
changed log dir
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3632 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:08:13 +00:00 |
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weisburd
|
fea8054e9e
|
Updated long name for -l to --run-locally
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3631 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 22:26:45 +00:00 |
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weisburd
|
72e669538e
|
Updated arg description for -s
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3629 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 22:04:01 +00:00 |
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weisburd
|
cef12b45e1
|
Fixed typo
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3561 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-15 21:17:14 +00:00 |
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weisburd
|
c0370f4d0a
|
Added both inclusive and exclusive filters
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3538 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-11 18:40:41 +00:00 |
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weisburd
|
d1a4c4f0d3
|
Added -w filter option allowing user to specify chromosomes to be skipped.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3531 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-10 20:58:25 +00:00 |
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weisburd
|
6fd2d39a7d
|
Modified run_locally mode to use os.system(..) instead of popen
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3515 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:10:03 +00:00 |
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weisburd
|
a3ccf49f5b
|
Write error to stderr
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3514 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:09:10 +00:00 |
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weisburd
|
2b31975cb4
|
Added more options for coordinate systems - now you can add 1 to either the start coordinates, the end coordinates, or both
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3508 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:49:19 +00:00 |
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weisburd
|
410afcdf2c
|
Added parallelization options - when running locally, multiple processes can be spawned, or a -nt arg can be specified to run each TranscriptToInfo instance multi-threaded
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3507 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:48:07 +00:00 |
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weisburd
|
92c72d3361
|
Added back lines that update the *big-table-header.txt file before using it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3506 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:45:41 +00:00 |
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weisburd
|
3c24223d02
|
Script for concatenating 2 AnnotatorInputTables, and writing the result to standard out. Merge-sorts the 2 tables while concatenating them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3505 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:44:16 +00:00 |
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depristo
|
f32a32269c
|
minor change for eric
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3418 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-21 20:13:36 +00:00 |
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depristo
|
d1098fa77b
|
Removing unnecessary dependences that were causing problems for Sendu
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3410 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-21 13:07:41 +00:00 |
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depristo
|
886e9c1297
|
Now can take a VCF file as input
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3378 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-18 17:06:12 +00:00 |
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depristo
|
2a212c497f
|
minor improvements and bug fixes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3376 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-18 15:54:42 +00:00 |