Added "lazy now" variant of Iso8601Date.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1573 8bce386e-0d6e-43e0-b1ca-608082c0432d
Implementation of a simple ped-file parser and writer for PED files that contain family/pheno information but no genotypes.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1574 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a couple of methods for 1) doing vector multiplication of two arrays and b) summing values in an array.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1575 8bce386e-0d6e-43e0-b1ca-608082c0432d
Made a few things static that were'nt, but needed to be.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1576 8bce386e-0d6e-43e0-b1ca-608082c0432d
Tided up a little bit and then added a method to be able to query by region from the VCFFileReader.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1577 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.101

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1578 8bce386e-0d6e-43e0-b1ca-608082c0432d
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.)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1581 8bce386e-0d6e-43e0-b1ca-608082c0432d
Do not check file termination if reading from a pipe.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1582 8bce386e-0d6e-43e0-b1ca-608082c0432d
Separating the VCF encoding functions from the VCFWriter class

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1583 8bce386e-0d6e-43e0-b1ca-608082c0432d
Change SeekableStreamFactory to a singleton

Allow an application to set the implementation of SeekableStreamFactory. Default implementation is the same.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1584 8bce386e-0d6e-43e0-b1ca-608082c0432d
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.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1585 8bce386e-0d6e-43e0-b1ca-608082c0432d
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).

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1586 8bce386e-0d6e-43e0-b1ca-608082c0432d
Bug fix: `IoUtil.slurp(java.io.File)` throws an exception unnecessarily when attempting to read empty files.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1587 8bce386e-0d6e-43e0-b1ca-608082c0432d
Make IlluminaTileMetrics inner class static and add another ctor so it can be used for writing TileMetricsOut in addition to reading.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1588 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.102

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1589 8bce386e-0d6e-43e0-b1ca-608082c0432d
Optionally compute MD5 on the fly when writing FASTQ in IlluminaBasecallsToFastq and SamToFastq, and write to companion file.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1592 8bce386e-0d6e-43e0-b1ca-608082c0432d