[Samtools-help] Picard release 1.78

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

Picard release 1.78
9 October 2012

- IlluminaBaseCallsToSam bug fixes:
   - Fix hang if a worker thread ran out of memory.
   - Fix bug in which failure of worker thread would result in 
successful program exit status.
   - Bug fix: Throw exception when barcodes that were not provided in 
libraray_params were read from tile.

- Fluidigm:
   - IlluminaUtil.java: Added adapters for fluidigm access array.
   - IlluminaBasecallsToSam.java: Added fluidigm access array adapters 
to the default set of adapter sequences to look for and trim.

- Make SamRecordIntervalIterator.close() idempotent.

- SAM header version number:
   - Change version number output in SAM text header to 1.4.
   - Change ViewSam so that it outputs whatever was the version number 
in the input, rather than always replacing with CURRENT_VERSION.

-Alec