[Samtools-announce] Picard release 1.114

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

Picard release 1.114
20 May 2014

Note: This is the first release based on GitHub code.  Generating this release was somewhat bumpy.  As usual, please let us know if you experience any problems.


- Complete reorganization of packages.  Map of old to new package names is forthcoming, but the basic change is "net.sf.samtools" => "htsjdk.samtools" and "net.sf.picard" => "picard."

- Enable `CollectTargetedPcrMetrics` and `CalculateHsMetrics` to target multiple baitsets.
  - Both command line programs' `TARGET_INTERVALS` argument accept multiple values.
  - `CalculateHsMetrics`'s `BAIT_INTERVALS` accepts multiple values.

- Add new modes to `IntervalListTools`.
  - `INTERVAL_SUBDIVISION`, which is the default mode, and functions like the previous version of `IntervalListTools`.
  - `BALANCING_WITHOUT_INTERVAL_SUBDIVISION`, which emits interval lists without splitting them up, and sizes the output interval list sizes to be no smaller than the largest input interval.

- Added an ASSUME_SORTED flag to FixMateInformation to allow grouped reads to be analyzed directly without prior sorting.

- IlluminaBasecallsConverter: Flush sorting collections when a barcode within a tile has completed to avoid running out of memory

- Add `SamReaderFactory` as a new facility for reading from SAM files.
  - Produces `SamReader` objects, which are similar to `SAMFileReader`.
  - Deprecate `SAMFileReader`, as `SamReaderFactory` is the preferred approach to creating things that read SAMs.  `SAMFileReader` still functions as normal.
  - See `SamReaderFactory`'s javadoc for examples of how to use it.


-Alec