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picard-tools-1.114.zip 2014-05-20 50.4 MB 11 weekly downloads
README.txt 2014-05-20 1.4 kB 11 weekly downloads
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.
Source: README.txt, updated 2014-05-20