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7 Commits (188c4f67b07fffae8e2c471ef1dd8de2fa40375b)

Author SHA1 Message Date
carneiro 7598f5f6a7 forgot to remove a debug line. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5246 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-15 16:25:48 +00:00
carneiro e45b699ac0 standardizing the name of the scripts and fixing some bugs with the remapping. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5245 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-15 16:19:58 +00:00
carneiro 5f10fffa47 merge intervals now prints a sorted list in the end. 
added the ccs datasets to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5233 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 20:57:59 +00:00
carneiro 50c2fa3c3a this -1 made ALL the difference in the world. Minor bug fix. 
Regular updates to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 19:25:09 +00:00
carneiro e7d38247bb chunkIntervals.lua creates 1Mb interval chunks out of any .intervals file. Useful for methods development pipeline datasets. 
remapAmplicons.lua takes a sam file with reads aligned to amplicon references, a reference genome , and an amplicon reference mapping table, and rewrites the sam file with mappings to the reference sequence.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 18:21:31 +00:00
carneiro aab0ec209b small bug fix on chromosome names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5168 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-01 20:55:19 +00:00
carneiro a2e2a6a9c3 A script to convert an intervals file into a sorted unoverlapping intervals file. Super fast implementation using multiple hashes, should do the job instantly no matter how big the intervals are. 
ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals file fixed before we can run Unified Genotyper because of scatter-gather.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5117 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-28 21:46:41 +00:00