[Samtools-announce] Picard Release 1.124 - NOTE - Change to CLP Invocation!

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

Picard release 1.124
3 November 2014

- Change Picard Command Line Programs to ALL execute from single JAR
    This makes a fundamental change to how we run Picard.  We now have a
    single JAR (command line program), rather than multiple JAR (one per
    tool). In this brave new world, the single command line program is given
    the the command line program name (ex. SamView) to specify which tool to
    run.  We also provide a convenient summary of all of the tools
    available.

    For the developers, we add a facility to add new command line programs
    to the single JAR, by extending the PicardCommandLine and adding the
    package name(s) for us to search for classes that extend
    CommandLineProgram.  The usage is now put in
    CommandLineProgramProperties, where we can also specify short usages
    (for the summary help message), program versions, and program groups.
    The latter is useful for grouping tools that operate on common filetypes
    or have similar function (ex. SAM/BAM).

    We made a number of new tools public, coming from our internal toolset.
    These include: BaitDesigner, CalculateReadGroupChecksum,
CheckTerminatorBlock,
    CollectIlluminaBasecallingMetrics, CollectIlluminaLaneMetrics,
    CollectJumpingLibraryMetrics, CollectOxoGMetrics,
    CollectQualityYieldMetrics, CollectRrbsMetrics, GatherVcfs,
    LiftOverIntervalList, ScatterIntervalsByNs, and SplitSamByLibrary.
    These may prove useful, or not.

- Changed Output of GenotypeConcordance tool
    Additional metrics file output which contains the raw counts of
contingency
    values (i.e. TP for true positives, FN for false negatives...)

- New CLP 'CollectIlluminaSummaryMetrics' to collect coverage information
    according to Illumina-defined filters.

- New CLP 'RenameSampleInVcf' to rename a sample in a VCF

- New CLP 'FilterVcf' that provides simple hard filtering functionality for
VCFs.

- Added ability to open SamReader from string, specifying either a URL or a
file path.
    This will make it easier treat INPUT parameters in Picard tools
uniformly regardless of
    whether they designate a file or URL resoures.  Url detection and
decision of whether
    the resource is file based on url based is done in SamInputResource.

- Some support for VCF v4.2 files added.
    Handles "Number=R" for INFO fileds in the header.
    Other VCF v4.2 specific additions (Eg: Source and Version fields in
INFO header lines) are not handled, but appear to be silently ignored.
    Tested on output of samtools mpileup | bcftools call (1.0-17-gfaf4dd6,
1.0-55-gc661821, using htslib 1.0-11-g830ea73)

- Bug fix: 'fixed the behavior of BCF2Utils.toList() when it's given an
array'
    Old version return a List with a single element, which was the provided
array.
      This broke BCF writing, in particular when a FORMAT annotation used
arrays instead of Lists
    Made toList generic, rather than returning a List<Object>
    Removed the redundant BCF2FieldEncoder.toList()
    Added unit tests

- Bug fix in Abstract AlignmentMerger
    Consider soft clipping at the ends of reads when clipping reads that
    overhang the reference

- Added a button to the explain-flags.html page.
    This button switches the flag from the value of a read, to that of its
mate
    (as much as can be inferred).

Enjoy!

George