asivache 2cab4c68d4 Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1898 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-22 14:55:07 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding.	2009-10-22 14:55:07 +00:00
test/org/broadinstitute/sting	Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated.	2009-10-21 21:18:26 +00:00