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Added an optional tag argument RodBind, similar to the Tag argument on TaggedFile. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5437 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-03-14 17:49:03 +00:00
parent 33c7593218
commit c18f1aa828
1 changed files with 13 additions and 5 deletions
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18
scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
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@ -7,20 +7,26 @@ import java.lang.String
/** /**
* Used to provide -B rodBind arguments to the GATK. * Used to provide -B rodBind arguments to the GATK.
*/ */
class RodBind(var trackName: String, var trackType: String, path: String) extends File(path) with FileExtension { class RodBind(var trackName: String, var trackType: String, path: String, val tag: String) extends File(path) with FileExtension {
def this(trackName: String, trackType: String, path: String) =
this(trackName, trackType, path, null)
def this(trackName: String, trackType: String, file: File, tag: String) =
this(trackName, trackType, file.getPath, tag)
def this(trackName: String, trackType: String, file: File) = def this(trackName: String, trackType: String, file: File) =
this(trackName, trackType, file.getPath) this(trackName, trackType, file.getPath, null)
require(trackName != null, "RodBind trackName cannot be null") require(trackName != null, "RodBind trackName cannot be null")
require(trackType != null, "RodBind trackType cannot be null") require(trackType != null, "RodBind trackType cannot be null")
def withPath(newPath: String) = new RodBind(trackName, trackType, newPath) def withPath(newPath: String) = new RodBind(trackName, trackType, newPath, tag)
} }
/** /**
* Used to provide -B rodBind arguments to the GATK. * Used to provide -B rodBind arguments to the GATK.
*/ */
object RodBind { object RodBind {
def apply(trackName: String, trackType: String, path: String) = new RodBind(trackName, trackType, path) def apply(trackName: String, trackType: String, path: String, tag: String) = new RodBind(trackName, trackType, path, tag)
def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file) def apply(trackName: String, trackType: String, path: String) = new RodBind(trackName, trackType, path, null)
def apply(trackName: String, trackType: String, file: File, tag: String) = new RodBind(trackName, trackType, file, tag)
def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file, null)
/** /**
* Formats the rod binding on the command line. * Formats the rod binding on the command line.
@ -33,6 +39,8 @@ object RodBind {
*/ */
def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = { def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
value match { value match {
case rodBind: RodBind if (rodBind.tag != null) =>
" %s:%s,%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath, rodBind.tag)
case rodBind: RodBind => case rodBind: RodBind =>
" %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath) " %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath)
} }