Merge branch 'mutect_version_check'
Remove intermediate trimmed files during cutadapt.
Documentation on developing with bcbio-nextgen and anaconda directory #147. Bump version to next development
Remove multiprocessing dependency from trimming.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added read_through change.
Provide better error messages and documentation when  not saved in configuration #148
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Link to contributor information from the start of the README. #147
Begin removing custom QC code in favor of full QC packages + supplement programs as needed. Integrates qualimap and eliminates custom pdflatex PDF generation
Remove pdflatex dependence and creation of custom PDF report file.
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
Provide clean recovery from sambamba index errors during high load, falling back to single core samtools indexing
Provide additional text in installation emphasizing usefulness of automated installer