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gatk-3.8/public/java/src/org/broadinstitute/sting/gatk/refdata
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Eric Banks d7d8b8e380 Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now. 2011-11-28 14:18:28 -05:00
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tracks Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now. 2011-11-28 14:18:28 -05:00
utils Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed. 2011-10-26 14:11:49 -04:00
RODRecordListImpl.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
ReadMetaDataTracker.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
RefMetaDataTracker.java Updating random walkers to new rod system; removing unused GenotypeAndValidateWalker 2011-08-15 14:05:23 -04:00
ReferenceDependentFeatureCodec.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ReferenceOrderedDatum.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SeekableRODIterator.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
VariantContextAdaptors.java Change interface to getNegLog10PError to getLog10PError 2011-11-18 21:07:30 -05:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00