8 Commits (3f75fc4e83c14346f4e8687f6e78692ee623d97f)

Author	SHA1	Message	Date
ebanks	2e89d5e46f	That was an annoying bug to find. Mark, I want a beer. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@293 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-03 20:05:24 +00:00
depristo	c1abcfb014	Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@291 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-03 19:53:33 +00:00
ebanks	42eb356782	1. modifed by read traversals with indexes to be more general ... 2. GenomeLocs for reads should have ends spanning the read (moved it to GenomeLoc from Utils) 3. Got rid of those stupid unmappable characters from comments in various files git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@289 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-03 18:24:08 +00:00
ebanks	4faa680887	*Massive* speed-up for interval-based by-read traversals. ... [Could do more optimizing, but this simple fix was good enough for now] git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@266 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-02 20:19:39 +00:00
hanna	7fda409f4e	Fixed bug where read traversals would fail with an exception when not called with a genome_region (-L) argument. From TraversalEngine, line 455, looks like Mark intended an invariant where the list of locations is 0 length if not specified. Made GenomeLoc code compliant with that. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@230 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-30 23:43:12 +00:00
depristo	d7c0bcc223	Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. ... All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20 Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use. Pileup now marks, very clearly, reference positions without covered reads. Made changes around the codebase to deal with new GenomeLoc structure. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-28 20:37:27 +00:00
depristo	ff98e28abf	High-performance interval list implement -- uses StringBuilder to avoid n^2 calculation. Can handle millions of locations quickly now ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@182 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 02:17:48 +00:00
hanna	63cd1fe201	Push core / playground lower into the tree. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-23 23:19:54 +00:00