zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/test/org/broadinstitute/sting
History
Eric Banks f172c349f6 Adding the functionality to enable users to input a file of VCFs for -V. 
To do this I have added a RodBindingCollection which can represent either a VCF or a
file of VCFs.  Note that e.g. SelectVariants allows a list of RodBindingCollections so
that one can intermix VCFs and VCF lists.

For VariantContext tags with a list, by default the tags for the -V argument are applied
unless overridden by the individual line.  In other words, any given line can have either
one token (the file path) or two tokens (the new tags and the file path).  For example:
foo.vcf
VCF,name=bar bar.vcf

Note that a VCF list file name must end with '.list'.

Added this functionality to CombineVariants, CombineReferenceCalculationVariants, and VariantRecalibrator.
 		2014-01-08 00:45:00 -05:00
..
commandline Adding the functionality to enable users to input a file of VCFs for -V. 2014-01-08 00:45:00 -05:00
gatk Fixed bug in the filtering of lifted over variants where a deletion at the end of a contig could cause it to error out. 2013-12-11 14:07:18 -05:00
jna Fix pipeline tests that were not respecting the pipeline test dry run setting 2013-06-28 15:27:17 -04:00
utils Write a new tool for spliting reads that have N cigar string. 2014-01-01 22:21:36 -05:00
BaseTest.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
ExampleToCopyUnitTest.java Add a class-based DataProvider 2013-12-03 13:31:01 -05:00
MD5DB.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
MD5Mismatch.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
WalkerTest.java Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy 2013-12-03 23:12:14 -05:00