create coverage table
add sample_id to composite key
coverageDB modules
populate CoverageDB from existing coverage files
populate CoverageDB by streaming directly from samtools
testing CoverageDB
only get coverage data for SNP positions and flanking (huge savings in time and disk space reqs)
build coverageDB by chromosome
cleanup
incorporate CoverageDB subroutines as methods in coverage_commander (first pass)
add forking for populating CoverageDB
add verbose output and TODO tasks
suppress useless mpileup output sent to stderr
update verbose progress statement
reduce forking for getting data from CoverageDB by half (due to overhead from samtools, etc.)
add script for testing 'get_coverage_db' method
Merge branch 'feature/database' into develop