[Samtools-announce] Picard release 1.128

[George G. <gg...@br...>]

Picard release 1.128
12 January 2015

 - Refactoring CollectWgsMetrics in order to be able to easily create
    CollectRawWGSMetrics.
 - Create RawWGSMetrics by overriding some default option values and
    repackaging the metrics class.
 - Moved CollectIlluminaSummaryMetrics (will be deleted eventually)
 - Fixed some test files.
 - Removed the buggy CLP CollectIlluminaSummaryMetrics.java and its test

 - Modified CommandLineParser class (and test) to fix overridable option
fields

 - Modified PicardCommandLine class
   - allow --list-commands to print all available commands to STDOUT
   - allow colors to be disabled with -Dpicard.cmdline.color_status=false

 - Modified Interval List Tool to add functionality so that it can use VCF
as a source for intervals

 - Modified VCFConstants - removing GATK-specific constants

 - Added test (SamSpecInTest) to check min/max values for i tag in SAM/BAM

 - Added input validation functions that can deal with both file and URL
inputs, in preparation for allowing GA4GH resources as inputs into Picard
tools.

 - Made static methods in TextCigarCodec and BinaryCigarCodec

 - isCRAMFile moved to SamStreams. Use readBytes instead of dis readFully

 - Fixed race condition in SAMFileWriterImpl  where synchronouslyClose()
would be called multiple times if AbstractAsyncWriter.close() called twice
simultaneously

 - Enhancements to VCFFileReader:
   - Added functionality so that fromVCF can create an intervalList with or
without filtered variants (defaulting to without, as currently)
   - Added functionality to fromVCF so that the intervals will end at the
END value from the info field (if available).

 - Make SortingVariantContextWriter public.
    - Currently, the only way to access this functionality is through
VariantContextWriterFactory.sortOnTheFly,
      but VariantContextWriterFactory is deprecated.

George