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gatk-3.8/java/test/org/broadinstitute/sting/utils
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hanna 4a33cdacde Some basic integration tests detecting breakage in OTF BAM index generation. 
Doing it manually for the moment so that there's at least something testing
this capability; will followup eventually with Mark to see whether we can
shape the VCF index generation code in such a way that it supports BAM index
testing as well.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5093 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-26 23:48:04 +00:00
..
baq Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
bed Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
collections Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
fasta Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
genotype Moving GLF code to archive 2011-01-15 22:42:42 +00:00
interval Some basic integration tests detecting breakage in OTF BAM index generation. 2011-01-26 23:48:04 +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 An apparently robust implementation of the file locking for distributed computation, using Lucene's file creation locking approach. It is worth trying out for those with large-scale, high-cost data sets. Details and discussion at group meeting on Wednesday. Some cleanup still needed. 2011-01-26 13:45:40 +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 vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler. 2011-01-12 17:32:27 +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