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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
History
Eric Banks de56134579 Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF. 
It didn't completely work before (it was hard-coded for a particular long-lost data set) but it should work now.
Since I thought that it might prove useful to others, I moved it to protected and added integration tests.

GERALDINE: NEW TOOL ALERT!
 		2014-01-15 13:49:31 -05:00
..
annotator The QD normalization for indels was busted and is now fixed. 2014-01-13 15:23:36 -05:00
beagle Simpler FILTER and info field encoding for BeagleOutputToVCF 2013-06-14 15:56:13 -04:00
bqsr Removed plots generation from the BaseRecalibration software 2013-06-19 14:47:56 -04:00
compression/reducereads Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int. 2013-11-27 18:55:03 -05:00
diagnostics Add GC Content to DiagnoseTargets 2013-12-03 23:04:40 -05:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper The QD normalization for indels was busted and is now fixed. 2014-01-13 15:23:36 -05:00
haplotypecaller The QD normalization for indels was busted and is now fixed. 2014-01-13 15:23:36 -05:00
indels Added in a check for what would be an empty allele after trimming. 2014-01-15 11:04:19 -05:00
phasing Add documentation for RBP, and also update the MD5 for the tests now that the output uses HP tags instead of '|', which is now reserved for trio-based phasing 2014-01-03 12:04:47 -05:00
rnaseq Write a new tool for spliting reads that have N cigar string. 2014-01-01 22:21:36 -05:00
simulatereads Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF. 2014-01-15 13:49:31 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval adding a check for the UNAVAILABLE case of GenotypeType in CountVariants 2013-08-29 17:27:00 -04:00
variantrecalibration Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file. 2014-01-02 14:46:04 -05:00
variantutils Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. 2013-12-31 12:07:56 -05:00