View source: R/phyloscan.fun.R
phsc.find.bam.and.references | R Documentation |
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
)
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. |
data.table with rows 'IND' (individual identifier), 'SAMPLE' (sample identifier), 'BAM' (bam file), and 'REF' (reference file).
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