Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
If flag selected at commandline would iterate through the file rather than pileup.
This would require a sorted input file check and a new method for iterating through the bam file.
Would give a large speed increase for input loci files with many concurrent or close clusters of positions.
If flag selected at commandline would iterate through the file rather than pileup. This would require a sorted input file check and a new method for iterating through the bam file.
Would give a large speed increase for input loci files with many concurrent or close clusters of positions.