gatk-3.8

Author	SHA1	Message	Date
chartl	544900aa99	Migration of some core calculations (log-likelihood probabilties, etc.) from CoverageAndPowerWalker into static methods in PoolUtils git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1527 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-03 21:43:29 +00:00
chartl	5130ca9b94	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1516 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-03 15:17:02 +00:00
chartl	8740124cda	@ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0. @MathUtils - added a new method: cumBinomialProbLog which calculates a cumulant from any start point to any end point using the BinomProbabilityLog calculation. @PoolUtils - added a new utility class specifically for items related to pooled sequencing. A major part of the power calculation is now to calculate powers independently by read direction. The only method in this class (currently) takes your reads and offsets, and splits them into two groups by read direction. @CoverageAndPowerWalker - completely rewritten to split coverage, median qualities, and power by read direction. Makes use of cumBinomialProbLog rather than doing that calculation within the object itself. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1462 348d0f76-0448-11de-a6fe-93d51630548a	2009-08-27 19:31:53 +00:00

Author

SHA1

Message

Date

chartl

Migration of some core calculations (log-likelihood probabilties, etc.) from CoverageAndPowerWalker into static methods in PoolUtils

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1527 348d0f76-0448-11de-a6fe-93d51630548a

2009-09-03 21:43:29 +00:00

chartl

5130ca9b94

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1516 348d0f76-0448-11de-a6fe-93d51630548a

2009-09-03 15:17:02 +00:00

chartl

8740124cda

@ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0.

@MathUtils - added a new method: cumBinomialProbLog which calculates a cumulant from any start point to any end point using the BinomProbabilityLog calculation.

@PoolUtils - added a new utility class specifically for items related to pooled sequencing. A major part of the power calculation is now to calculate powers
             independently by read direction. The only method in this class (currently) takes your reads and offsets, and splits them into two groups
             by read direction.

@CoverageAndPowerWalker - completely rewritten to split coverage, median qualities, and power by read direction. Makes use of cumBinomialProbLog rather than
                          doing that calculation within the object itself.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1462 348d0f76-0448-11de-a6fe-93d51630548a

2009-08-27 19:31:53 +00:00

3 Commits (544900aa99454759b34029f5125296d26a2853f2)