chartl 61d5daa65c EXTREME interval processing. Still undergoing testing. ... + GroupIntervals allows user-defined scattering (e.g. take an interval list file, split it into k smaller interval list files by number of lines) + ExpandIntervals expands the intervals, either by widening them, or allowing the definition for nearby intervals (e.g. flanks starting 1bp before and after, ending 10bp after that) + IntersectIntervals takes n interval lists, writes 1 interval list that is the n-way intersection of all of them git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4885 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-20 19:42:50 +00:00
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chartl	EXTREME interval processing. Still undergoing testing.	2010-12-20 19:42:50 +00:00
depristo	Experimental support for sided annotations. Currently not more/less valuable than two-tailed testing. Future experiments are needed	2010-12-17 15:08:31 +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	Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:	2010-12-10 04:36:06 +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	Updating the NA12878.HiSeq bam file to be the correct bam file in the methods development qscript.	2010-12-20 14:53:10 +00:00
fullCallingPipeline.q	Adding a window size variable to avoid indel genotyper error	2010-12-18 04:19:54 +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