Picard release 1.44
24 April 2011
- Fix bug in SeekableFileStream. read() should return -1 if nothing could be read due to EOF. Fix courtesy of Matt Mead.
- Added new programs IlluminaBasecallsToSam, ExtractIlluminaBarcodes, and supporting classes, utilities, and tests. ExtractIlluminaBarcodes reads Illumina data and selects the best-matching molecular barcode for each read. IlluminaBasecallsToSam converts Illumina data into SAM format.
- MarkDuplicates.java: Do not consider non-primary alignments as potential duplicates.