• Made unpaired reads not fall through to paired read checks (#1133)
• illumina directory return code conforms to posix standards
• CrosscheckFingerprint speedup, extra functionality and NIO enabling (#1086)
• Refactor SamToFastq and add SamToFastqWithTags (#1110)
• Change order of iteration in pickTranscripts for speed. (#1126)
• Add IdentifyContaminant CLP (#1107)