Picard release 1.60
17 January 2012
- Modified ExtractIlluminaBarcodes to handle dual barcodes. Metrics file contains barcode read bases separate by slashes, barcode.txt files concatenate all the barcode read bases with no separator. Removed BUSTARD_DIR option, which has been deprecated in favor of BASECALLS_DIR.
- Eliminate SamFileHeaderMerger.addIterator, and instead add another ctor that allows for passing iterators in the ctor. Use LinkedHashMap instead of ArrayList in SamFileHeaderMerger for speed. Patch courtesy of Matt Hanna.
- FilteringIterator.java: assert that reads are in SortOrder.queryname when filtering pairs
- SamToFastq.java: Added a little progress logging to SamToFastq.