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gatk-3.8/java/test/org/broadinstitute/sting/utils
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hanna acfe83920b '-L unmapped': adding integration tests for explicitly including (-L unmapped) 
unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.

'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-15 23:11:46 +00:00
..
baq Trival fix to broken build 2010-12-11 13:56:03 +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 '-L unmapped': adding integration tests for explicitly including (-L unmapped) 2010-12-15 23:11:46 +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 Getting back to '-L unmapped': 2010-12-14 18:24:18 +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