Map IntervalList format column four to feature name

[heuermh]

Fixes #1152, #1168

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GitHub pull request #1159 of commit e1b6772 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1159/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6d7e26f # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1159/merge^{commit} # timeout=10Checking out Revision 6d7e26f (origin/pr/1159/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6d7e26f9c46f4086de5bd3974336b0ae56d35520First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[fnothaft]

As an aside, I feel like we've got enough of this patten (print error message if STRICT, log if LENIENT, and return None if not STRICT) around where we might as well wrap it up into a function and factor it out.

[heuermh]

The way I'm seeing it, if it were made a function, the error messages would always be formatted.

[fnothaft]

How so?

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[fnothaft]

We should try/catch around the fields(x).toLong/fields(x).toDouble calls, both here and below and above and everywhere. We could factor it out like so:

def checkAndSet[T](field: String,
  convFn: String => T,
  setFn: T => Unit,
  stringency: ValidationStringency) {
  try {
    val t = convFn(field)
    setFn(t)
  } catch {
    case e: Throwable => {
      if (stringency == ValidationStringency.LENIENT) {
        log.warn("Failed to convert %s.".format(field))
      } else if (stringency == ValidationStringency.STRICT) {
        throw new IllegalArgumentException("Setting field from %s failed with %s.".format(
          field,
          e.msg))
      }
    }
  }
}

Perhaps we factor this out into a trait:

sealed trait FeatureConverterCanBeValidated {
  val stringency: ValidationStringency

  def validateOrNone(...): Option[Feature]

  def checkAndSet[T](field: String,
    convFn: String => T,
    setFn: T => Unit)
}

All of the classes in here could be turned into case classes that extend that trait. What do you think? Should you proceed, the trait name I proposed is terrible, so please change it.

[heuermh]

Will check to see what htsjdk does with NumberFormatExceptions and validation stringency.

[heuermh]

This seems to fiddly to me, so I've punted for now

[fnothaft]

Generally LGTM! Thanks for taking this on @heuermh. I've dropped a variety of line notes inline.

[heuermh]

Addressed some review comments and rebased.

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[fnothaft]

LGTM! I will leave this open until Friday morning to wait for any further review comments.

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[fnothaft]

Thanks @heuermh! Merged as 53b8f48 and dff43ef.

[heuermh]

Thanks!