• Add tools to be documented + minor tweaks to MD docs
• Small typo in IlluminaBasecallsToSam doc.
• Adding an option to output an concordance state annotated VCF in GenotypeConcordance.
• Fix the same variant returned multiple times by ByIntervalListVariantContextIterator.
• new CLP: FindMendelianViolations (#536)
• Fix for MergeBamAlignment when one read maps to both pos and neg strand
• updating gradle from 2.13 -> 3.1 (#680)
• • moved FindMendelianViolations from the private repository - added a test - cleaned up the code a-la-java8
• update htsjdk to 2.7.0 (#681)
• Include low quality bases in the base quality histogram and add a new coverage histogram that includes these bases in order to improve theoretical het sensitivity estimates.
• delete unused imports, change year in license
• rename utils methods in tests
• add license to tests
• added tests for both algorithms
• migrate elc first version of algorithm