Find bam and corresponding reference files

This function finds bam and corresponding reference files in a given directory, and groups them by a common sample ID as well as by an individual ID.

phsc.find.bam.and.references(data.dir,
  regex.person = "^([A-Z0-9]+-[A-Z0-9]+)-.*$", regex.bam = "^(.*)\\.bam$",
  regex.ref = "^(.*)_ref\\.fasta$", verbose = 1)

Arguments

data.dir	Full path of data directory
regex.person	Regular expression with one set of round brackets, which identifies the person ID in the file name of bams and references
regex.bam	Regular expression that identifies bam files, with one set of round brackets that identifies the sample ID.
regex.ref	Regular expression that identifies ref files, with one set of round brackets that identifies the sample ID.

Value

data.table with rows 'IND' (individual identifier), 'SAMPLE' (sample identifier), 'BAM' (bam file), and 'REF' (reference file).