fgbio

Type Members

1. class CallDuplexConsensusReads extends FgBioTask with Pipe[SamOrBam, SamOrBam]

   

2. class CallMolecularConsensusReads extends FgBioTask with Pipe[SamOrBam, SamOrBam]

   

   Task to run CallMolecularConsensusReads on a BAM file that has been run through GroupReadsByUmi already.

   Task to run CallMolecularConsensusReads on a BAM file that has been run through GroupReadsByUmi already. Produces an unmapped BAM file!

3. class ClipOverlappingReads extends FgBioTask

   

4. class CollectDuplexSeqMetrics extends FgBioTask with PipeIn[SamOrBam]

   

5. case class ErrorRateByReadPosition(in: PathToBam, out: Option[PathPrefix] = None, ref: PathToFasta, variants: Option[PathToVcf], intervals: Option[PathToIntervals], includeDuplicates: Option[Boolean] = None, minMappingQuality: Option[Int] = None, minBaseQuality: Option[Int] = None) extends FgBioTask with Product with Serializable

   

6. class ExtractUmisFromBam extends FgBioTask with Pipe[SamOrBam, SamOrBam]

   

7. abstract class FgBioTask extends ProcessTask with JarTask with FixedResources with Configuration

   

   Base Task for any task in the FgBio jar.

8. case class FilterConsensusReads(in: PathToBam, out: PathToBam, ref: com.fulcrumgenomics.commons.CommonsDef.PathToFasta, minReads: Seq[Int], maxReadErrorRate: Seq[Double], maxBaseErrorRate: Seq[Double], minQuality: Int, maxNoCallFraction: Double) extends FgBioTask with Product with Serializable

   

9. case class FilterSomaticVcf(in: PathToVcf, bam: PathToBam, out: PathToVcf, sample: Option[String] = None, minMapQ: Option[Int] = None, minBaseQuality: Option[Int] = None, pairedReadsOnly: Option[Boolean] = None, endRepairDistance: Option[Int] = None, endRepairPValue: Option[Double] = None) extends FgBioTask with Product with Serializable

   

10. class GroupReadsByUmi extends FgBioTask with Pipe[SamOrBam, SamOrBam]

    

    Task to invoke GroupReadsByUmi.

11. class RemoveSamTags extends FgBioTask

    

12. class TrimFastq extends FgBioTask

    

13. class TrimPrimers extends FgBioTask