• • removed a O(maxCoverage * nLoci) sanity test which significantly increases run-time for CollectWgsMetrics when the maxCoverage is large, as it is by default for CollectRawWgsMetrics. (#716)
• Fix to handle overlapped read clipping in MergeBamAlignment when clipping already present (#709)
• • correcting DUAL_INDEXED adapter sequence according to the documentation (page 17 of http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf) and also inspection of read sequence from short inserts. (#705)
• Default output for CreateSequenceDictionary (#712)
• • remove reference to @deprecated VariantContextWriterFactory in htsdjk prior to removal from that codebase. (#710)
• Fix for issues 342 and 138: introduced ALSO_IGNORE_DUPLICATES option (#646)
• CollectIlluminaBasecallingMetrics supports an alternative barcodes (#702)
• • use SEQUENCE_REFERENCE when opening files in CheckFingerprints. This should allow fingerprinting CRAM files directly. (#703)
• Support in-line skips and molecular barcodes. (#697)
• The molecular indexes should be joined with hyphens rather than (#689)
• Fix for issue #432 CreateSequenceDictionary stalls indefinitely with large genomes (#687)