7 Commits (f12d40dde8ad0322c0d0614d935b95f9e2516aaa)

Author	SHA1	Message	Date
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
depristo	d952790258	GFF now parses attributes correctly and efficiently. Slightly better interface to Utils.join ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@253 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-01 22:54:38 +00:00
depristo	385736469c	High performance pileup code and utilities ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@242 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-01 00:47:47 +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
aaron	230c1ad161	moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@211 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-27 14:02:55 +00:00
depristo	d11bb0fc64	Added xReadLines class to utils. It is a iterator<string> and iterable<string> so you can easily read all lines from a file. It's been used to simplify the code to process intervals, and will be used to add merging data support to the system... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@187 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 15:17:38 +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