f962039273
Using James P's patch for the liftover script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4515 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-18 01:44:54 +00:00
e6d038067b
cleanup the temp index too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4512 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-17 04:41:42 +00:00
7aa030a9a4
Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4510 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-17 02:54:12 +00:00
3d988576a6
updated liftover script: it no longer needs to re-sort the vcf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4501 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 08:03:41 +00:00
7f1e44b764
update the example: /broad/1KG doesn't exist anymore
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4429 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-05 13:50:24 +00:00
a7af605d95
update to use new rod syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4119 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 20:21:53 +00:00
e50627a49e
1. Updated tests and added integration test for liftover code.
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2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 17:58:18 +00:00
15a6be5d50
Updated to reflect Mark's renaming binge
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3697 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 22:48:42 +00:00
22abbc0edb
Stupid cent_os doesn't allow old style 'sort' conventions. Updating liftover script...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3577 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 13:44:03 +00:00
7cab994d88
Add argument to sortByRef for specifying the tmp directory for sorting.
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Update the liftover script to reflect this addition.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3323 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:53:26 +00:00
bfc58c70fa
Adding newline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3322 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:08:08 +00:00
44de92e09d
Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 12:31:56 +00:00
ebanks