depristo 16e1bbd380 Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested. ... BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-08 01:01:39 +00:00
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baq	Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested.	2010-12-08 01:01:39 +00:00
bed	Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.	2010-12-05 18:29:39 +00:00
collections	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
fasta	Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.	2010-12-05 18:29:39 +00:00
genotype	Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.	2010-12-05 18:29:39 +00:00
interval	Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.	2010-12-05 18:29:39 +00:00
pileup	Stop RBP.getPileupBySample() from throwing a NullPointerException if the	2010-11-23 05:17:06 +00:00
report	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
sam	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
threading	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
BaseUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
GenomeLocParserUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
GenomeLocSortedSetUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
GenomeLocUnitTest.java	Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.	2010-12-05 18:29:39 +00:00
MathUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
PathUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
ReservoirDownsamplerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
UtilsUnitTest.java	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +00:00