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.
- 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.