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picard-tools-1.102.zip 2013-11-04 46.0 MB 0
README.txt 2013-11-04 1.5 kB 0
Totals: 2 Items   46.0 MB
Picard release 1.102 4 November 2013 - Changed default read name header formatting for fastq records emitted by `IlluminaBasecallsToFastq` to include new values and, in particular, passing-filter flags. The old read name header formatting is referred to as "Illumina," and the new formatting "Casava 1.8". This change necessitated adding two new required (by default) arguments: FLOWCELL_BARCODE and MACHINE_NAME. You may control the formatting emitted by IlluminaBasecallsToFastq with the `READ_NAME_FORMAT` argument. (For example, pass READ_NAME_FORMAT=ILLUMINA to emulate default functionality prior to this commit.) - ValidateSamFile.java: Do not check file termination if reading from a pipe. - Separating the VCF encoding functions from the VCFWriter class. - Change SeekableStreamFactory to a singleton. Allow an application to set the implementation of SeekableStreamFactory. Default implementation is the same. - Moved `VariantContextUtil`'s `calcVCFGenotypeKeys` and a field member into `VariantContext` to avoid referencing `VariantContextUtils` in some command-line programs. Referencing `VariantContextUtils` can cause `ClassInitializationException`s because it references jexl packages which do dynamic class-loading. This is more of a band-aid than a fix. - MakeSitesOnlyVcf.java: Bug fix: do not call `VCFHeader` constructor that copies sample names, since that forces the writer to emit genotype data for those samples (which fails the requirements of a site-only VCF).
Source: README.txt, updated 2013-11-04

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