Picard release 1.112
21 April 2014
- AbstractVCFCodec.java: Add ability to remap sample names for single-sample vcfs to the vcf codec.
By calling setRemappedSampleName() on an instance of a vcf codec, you instruct it to replace the existing sample name in the vcf header with a new value. Attempting to use this feature with multi-sample or sites-only vcfs throws an error.
- Make TextTagCodec.java and TagValueAndUnsignedArrayFlag.java public
- Move BLOCK_COMPRESSED_EXTENSIONS to Tribble so all projects use the same set of extensions.
- Create Tabix indices for block-compressed VCFs
- Deprecate VariantContextWriterFactory. Convert uses of VariantContextWriterFactory to VariantContextWriterBuilder.