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gatk-3.8/java/test/org/broadinstitute/sting
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hanna 83b8676b69 Hack to fix mysterious disappearing read attributes. Ultimately caused 
by the fact that the GATKSAMRecord, by design, needs to both inherit from 
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.

Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation.  But in 
the short-term, there's no obvious fix.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-13 19:06:54 +00:00
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alignment all fixed..thanks Matt! 2010-09-10 06:18:59 +00:00
commandline Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
datasources/pipeline Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
gatk Hack to fix mysterious disappearing read attributes. Ultimately caused 2010-10-13 19:06:54 +00:00
oneoffprojects/walkers The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder. 2010-09-21 18:21:22 +00:00
playground/gatk/walkers Recent changes to the build system make the build system complain loudly about 2010-09-24 22:09:12 +00:00
utils High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file. 2010-10-08 19:53:21 +00:00
BaseTest.java Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality. 2010-10-06 18:29:56 +00:00
WalkerTest.java High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file. 2010-10-08 19:53:21 +00:00