Picard release 1.114
20 May 2014
- 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.