rpoplin 61e848c4f0 It's clear from Sendu's calling and my own calling that -qScale 100.0 is a much better default value for low pass data. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4248 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-10 01:47:21 +00:00
..
alignment	- Fix our private repository of bwa reference support files.	2010-09-10 00:29:26 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	It's clear from Sendu's calling and my own calling that -qScale 100.0 is a much better default value for low pass data.	2010-09-10 01:47:21 +00:00
oneoffprojects/walkers	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
playground	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
utils	Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works.	2010-09-01 22:24:50 +00:00
BaseTest.java	VR integration tests are longer but much more useful.	2010-09-03 15:50:19 +00:00
WalkerTest.java	Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate.	2010-09-09 11:32:20 +00:00