[Samtools-help] Picard release 1.112

[Alec W. <al...@br...>]

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.

-Alec