6 Commits (3e7802a3e0786ec56b7b2a1e41dccfbc2279b78c)

Author	SHA1	Message	Date
chartl	3e7802a3e0	Minor changes to a qscript and the GQ constants on PrivatePermutations ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4956 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-07 18:26:21 +00:00
chartl	2235245af0	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). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4894 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-22 15:16:15 +00:00
chartl	80770dc032	Expanded target pipeline complete. Stop trying to be clever about scatter-gather; wait until functional SG is built-in to Q. Til then, a lazy version of the fullCallingPipeline. Seems to take a long time to generate the graph though... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4888 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-21 00:56:16 +00:00
chartl	fc33901810	Graph structure must be known at compile time. Removing GroupIntervals until a future point where in-process-functions can predict their output based on inputs [though this is probably forever: the inputs may not exist at compile time!] ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4886 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-20 21:22:58 +00:00
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
chartl	8118a439c0	Commit for Khalid ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4876 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-18 22:24:18 +00:00