• Home
• org.hammerlab.genomics
• readsets_2.10
• 1.0.3
• source code
• ReferenceArgs.scala

×

Project download

Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance.
Project price only 1 $

You can buy this project and download/modify it how often you want.

org.hammerlab.genomics.readsets.args.ReferenceArgs.scala Maven / Gradle / Ivy

package org.hammerlab.genomics.readsets.args

import org.kohsuke.args4j.{ Option ⇒ Args4jOption }

trait HasReference {
  def referencePath: String
  def referenceIsPartial: Boolean
}

trait ReferenceArgs extends HasReference {
  @Args4jOption(
    name = "--reference",
    required = true,
    usage = "Local path to a reference FASTA file"
  )
  var referencePath: String = _

  @Args4jOption(
    name = "--partial-reference",
    usage = "Treat the reference fasta as a \"partial FASTA\", comprised of segments (possibly in the interior) of contigs."
  )
  var referenceIsPartial: Boolean = false
}