Checking in initial bamcheck_base_content_peaks.R, copied from bamcheck_indel_peaks.R
Fixed max.contiguous when there are no true values in the vector (now returns 0 for start, end, and contiguous.cycles)
Implemented various checks of base content deviation.
Merge branch 'feature/base_content_peaks' into develop
Beginnings of packagification under the name bamcheckr
Added empty testthat test framework.
Working read_bamcheck and write_bamcheck (no longer using pipe to grep)
Dropped section column from internal data structure
Ported base content deviation to work with bamcheck format
Ports quality dropoff to read_bamcheck format
Fixes indel_peaks to work with bamcheck data from read_bamcheck
Moved remove_rightmost_missing_columns to common
Eliminates SN column from base_content_deviation, indel_peaks, quality_dropoff
Adds colons to SN variable for quality dropoff and base content deviation
Fixes bug in which read_bamcheck was reading a test file rather than the one passed in as an arg
Added stringr to import namespace
Added provenance to header
Added bamcheckr exports to NAMESPACE
Added outplotbase option to indel_peaks (although plots are not implemented)
Added [-h|--help] to basic usage statement