In JVM Task that pulls the total number of reads from the quality yield metrics file, and calculates a downsampling fraction.
Simple tasks that deletes one or more extent files.
Deletes one or more VCFs and their associated index files.
Gets the sample names from a VCF
Indexes a VCF.gz using tabix
Creates a directory along with any non-existent parents.
Creates a directory along with any non-existent parents. Returns 0 if the directory exists after running (including if it already existed), 1 otherwise.
Uses the shell to move a file or directory from one path to another
Class for running verifyBamID on sequence data in genotype-free mode.
Tabix (https://github.com/samtools/htslib)
Simple tasks that deletes one or more extent files. If a path represents a directory then the directory and all of it's children will be deleted.