weisburd
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e7939f7036
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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
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1cb8f51f8c
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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
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3cd0570c1e
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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
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dae3ce2c0f
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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
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fea8054e9e
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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
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72e669538e
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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
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cef12b45e1
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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
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c0370f4d0a
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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
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d1a4c4f0d3
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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
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6fd2d39a7d
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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
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a3ccf49f5b
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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
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2b31975cb4
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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
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410afcdf2c
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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
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92c72d3361
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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
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3c24223d02
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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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weisburd
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04e14ef85a
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Refactored so it could be used for knownGene and CCDS as well as refGene
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3373 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-18 02:45:11 +00:00 |
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weisburd
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f120a00433
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Fixed bug so that the strand, alternate, and reference columns are now moved correctly
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3342 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-10 17:59:39 +00:00 |
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weisburd
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a462b5e1e7
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Changed a default path
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3291 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-03 17:07:21 +00:00 |
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weisburd
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28f746b76a
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Added option to generate UCSC or NCBI sequence
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3283 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 17:26:00 +00:00 |
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weisburd
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c214056d88
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Script for concatenating results of GenerateTranscriptToInfo.py into one big file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3279 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:47:08 +00:00 |
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weisburd
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0069cb426d
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Script for spawning LSF jobs that run the TranscriptToInfo.java walker on each of the 50 contigs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3277 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:27:52 +00:00 |
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weisburd
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ba7fe7c4e1
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Renamed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3276 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:25:07 +00:00 |
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weisburd
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4937295a0b
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Renamed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3275 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:24:56 +00:00 |
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weisburd
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c7b4f78316
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Added -m arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3233 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-21 22:38:47 +00:00 |
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weisburd
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04c22a6640
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Added handling of UCSC and NCBI reference sequences
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3165 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-14 14:40:31 +00:00 |
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weisburd
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2183f10a1d
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Script for validating and converting text files into the tabular format required for GenomicAnnotator -B inputs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3156 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-13 13:35:10 +00:00 |