gatk-3.8

Commit Graph

Author	SHA1	Message	Date
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	cfee59e0e6	New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-27 15:40:45 +00:00

Author

SHA1

Message

Date

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

cfee59e0e6

New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a

2009-03-27 15:40:45 +00:00

2 Commits (ba99e9f6487f9e028837e7b45ef2ed2b8b065f77)