misc

Type Members

1. class CalculateDownsamplingProportion extends SimpleInJvmTask

   

   In JVM Task that pulls the total number of reads from the quality yield metrics file, and calculates a downsampling fraction.

2. class DeleteFiles extends SimpleInJvmTask

   

   Simple tasks that deletes one or more extent files.

   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.

3. class DeleteVcfs extends SimpleInJvmTask

   

   Deletes one or more VCFs and their associated index files.

4. class GetNumPfReads extends SimpleInJvmTask

   

5. class GetSampleNamesFromVcf extends SimpleInJvmTask

   

   Gets the sample names from a VCF

6. class IndexVcfGz extends ShellCommand

   

   Indexes a VCF.gz using tabix

7. class MoveFile extends ShellCommand

   

   Uses the shell to move a file or directory from one path to another

8. class VerifyBamId extends ProcessTask with Configuration with FixedResources

   

   Class for running verifyBamID on sequence data in genotype-free mode.