asivache 0d347d662a More plumbing: if after the shift window contains indel(s) at the first position, do not throw an exception, just print the warning (we can not deal with this situation!!) and discard those indels without trying to call them. This situation will most probably arise after forced shift over a messy region anyway. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2781 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-04 21:06:28 +00:00
..
arguments	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
contexts	added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine.	2010-01-27 05:17:01 +00:00
datasources	1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files.	2010-02-04 04:12:49 +00:00
examples	Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.	2009-12-13 04:13:30 +00:00
executive	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
filters	Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark.	2010-01-03 21:31:04 +00:00
io	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
iterators	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00
refdata	Will now work with simplest tabular format - genotype string ("+ACTT") does not have to be followed by ':'	2010-02-01 15:40:01 +00:00
traversals	VariantEval2 test framework implemented; Kiran is experimenting with the system. Not for use by anyone else. VariantContext appears to work well; I'll release it next week for general use following docs of the functions. Removing newvarianteval and other classes to avoid any future confusion. Update to TraverseLoci and RodLocusView to simplify a few functions and to correct some minor errors. All tests pass without modification.	2010-01-30 20:51:24 +00:00
walkers	More plumbing: if after the shift window contains indel(s) at the first position, do not throw an exception, just print the warning (we can not deal with this situation!!) and discard those indels without trying to call them. This situation will most probably arise after forced shift over a messy region anyway.	2010-02-04 21:06:28 +00:00
CommandLineExecutable.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
CommandLineGATK.java	Update our error messages to point to getsatisfaction.com/gsa.	2010-01-27 19:16:28 +00:00
GenomeAnalysisEngine.java	1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files.	2010-02-04 04:12:49 +00:00
Reads.java	changes to intelligently log overflowing locus pile-ups.	2010-01-20 08:09:48 +00:00
WalkerManager.java	Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built.	2010-01-20 19:18:19 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00