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depristo 5265f943b0 phasing per sample. tmp checkin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4898 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-22 20:14:06 +00:00
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chartl PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec). 2010-12-22 15:16:15 +00:00
depristo phasing per sample. tmp checkin 2010-12-22 20:14:06 +00:00
examples - After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list. 2010-10-21 06:37:28 +00:00
hanna Trying out Queue for the first time. 2010-11-18 18:29:12 +00:00
kshakir Checking in scripts used for testing the linear index MAX_FEATURES_PER_BIN. 2010-12-20 21:25:36 +00:00
lib Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires. 2010-12-15 03:33:36 +00:00
rpoplin Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers. 2010-12-21 21:14:20 +00:00
fullCallingPipeline.q Updated dbsnp version usage. Calling with 132, but still using 129 for eval to maintain consistant known/novel eval 2010-12-22 17:37:27 +00:00
recalibrate.scala - After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list. 2010-10-21 06:37:28 +00:00