Parse qualimap output HTML to provide high level summary metrics. Convert metrics file into more general YAML instead of variant specific CSV. Handle BED3 input to qualimap
Include variant calling statistics in final support output leveraging gemini. Add target region information from qualimap
Parse RNA-SeQC metrics and report as part of final project summary. Finalizes new QC and reporting structure
Have tophat get transcriptome index or GTF file from genome-resources yaml.
Merge pull request #150 from porterjamesj/aligner-genome-resources

Have tophat get transcriptome index or GTF file from genome-resources yaml.
Add tophat pre-computed transcriptome indexes to default genome resources files. Bump resource file versions for new retrieval. #150
Encapulate BAM indexing in a single function and switch to using sambamba for indexing to make use of multiple cores