v1.3.r6

• --sv_vcf argument which allows users to augment AA's SV detection with their own SV calls provided in a VCF format. This does not remove SVs discovered by AA. It only adds those from the VCF not already found by AA.
• --sv_vcf_no_filter to permit calls from --sv_vcf even if they are not set to 'PASS' or '.' .
• Automated protection against improperly-formatted inputs
• Reduces bugs created when AA is rerun into the same directory with existing files having the same sample name but launched with different input files.
• Bugfix for edge case where AA does not properly expand a newly discovered interval if a discovered SV lands exactly on the endpoint of the explored interval.
• Refactor Readme and standalone install info
• Provide explicit LICENSE file