Matt Hanna 5b58fe741a Retiring Picard customizations for async I/O and cleaning up parts of the code to use common Picard utilities I recently discovered. ... Also embedded bug fix for issues reading sparse shards and did some cleanup based on comments during BAM reading code transition meetings.		2012-02-08 08:34:37 -05:00
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R	queueJobReport now compresses PDF when running R 2.13+.	2012-01-10 17:32:30 -05:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
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java	Retiring Picard customizations for async I/O and cleaning up parts of the code to use common Picard utilities I recently discovered.	2012-02-08 08:34:37 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Introducing: VariantsToPed, the world's most annoying walker! And also a busted QScript to run it that I need Khalid's help debugging ( frownie face ). Note that VariantsToPed and PlinkSeq generate the same binary file (up to strand flips...thanks PlinkSeq), so I know it's working properly. Hooray!	2012-02-01 10:39:03 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00