9 Commits (a648b5e65e8ce2f64fddc5fef4017d7de15f39fb)

Author	SHA1	Message	Date
Mark DePristo	40431890be	-- BCF2 is now a reference dependent codec so it can initialize the contigs in the case where the file doesn't have contigs in it ... -- BCF2 writer can now work without the contig lines being in the header -- Made GenomeLocParser a final class	2012-05-24 10:57:06 -04:00
Guillermo del Angel	252e0f3d0a	Merged bug fix from Stable into Unstable	2011-12-08 13:11:39 -05:00
Guillermo del Angel	1bfe28067f	Don't try to genotype an indel even bigger than the reference window size, or else we'll be out of bounds. Necessary to handle Phase 1 integrated callset with large deletions. Better error indication when validating a GenomeLoc.	2011-12-08 12:54:08 -05:00
Eric Banks	022832bd74	Very bad use of the == operator with Strings was ensuring that validating GenomeLocs was very inefficient. This fix resulted in a significant speedup for a simple RodWalker.	2011-11-21 14:49:47 -05:00
Khalid Shakir	c50274e02e	During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. ... Moved flanking interval utilies to IntervalUtils with UnitTests.	2011-11-17 13:56:42 -05:00
Mark DePristo	dc4932f93d	VariantEval module to stratify the variants by whether they overlap an interval set ... The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like: -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants. Minor improvements to create() interval in GenomeLocParser.	2011-11-10 10:58:40 -05:00
Mark DePristo	800bb97f0b	Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser ... Updated all walkers that used the now deleted methods.	2011-08-03 16:04:51 -04:00
Mark DePristo	9992c373be	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00