Add --id and --id-file option

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -26,6 +26,7 @@ import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 import scala.collection.JavaConversions._
+import scala.io.Source
 
 class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
   javaMainClass = getClass.getName
@@ -69,7 +70,8 @@ object VcfFilter extends ToolCommand {
                   diffGenotype: List[(String, String)] = Nil,
                   filterHetVarToHomVar: List[(String, String)] = Nil,
                   filterRefCalls: Boolean = false,
-                  filterNoCalls: Boolean = false) extends AbstractArgs
+                  filterNoCalls: Boolean = false,
+                  iDset: Set[String] = Set()) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('I', "inputVcf") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
@@ -116,6 +118,12 @@ object VcfFilter extends ToolCommand {
     opt[Double]("minQualscore") unbounded () action { (x, c) =>
       c.copy(minQualscore = Some(x))
     } text ("Min qual score")
+    opt[String]("id") unbounded () action { (x, c) =>
+      c.copy(iDset = c.iDset + x)
+    } text ("Id that may pass the filter")
+    opt[File]("id-file") unbounded () action { (x, c) =>
+      c.copy(iDset = c.iDset ++ Source.fromFile(x).getLines())
+    } text ("File that contain list of IDs to get from vcf file")
   }
 
   var commandArgs: Args = _
@@ -124,6 +132,7 @@ object VcfFilter extends ToolCommand {
    * @param args the command line arguments
    */
   def main(args: Array[String]): Unit = {
+    logger.info("Start")
     val argsParser = new OptParser
     commandArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
 
@@ -132,6 +141,8 @@ object VcfFilter extends ToolCommand {
     val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(commandArgs.outputVcf).build)
     writer.writeHeader(header)
 
+    var counterTotal = 0
+    var counterLeft = 0
     for (record <- reader) {
       if (minQualscore(record) &&
         filterRefCalls(record) &&
@@ -143,12 +154,18 @@ object VcfFilter extends ToolCommand {
         mustHaveVariant(record) &&
         notSameGenotype(record) &&
         filterHetVarToHomVar(record) &&
-        denovoInSample(record)) {
+        denovoInSample(record) &&
+        inIdSet(record)) {
         writer.add(record)
+        counterLeft += 1
       }
+      counterTotal += 1
+      if (counterTotal % 100000 == 0) logger.info(counterTotal + " variants processed, " + counterLeft + " left")
     }
+    logger.info(counterTotal + " variants processed, " + counterLeft + " left")
     reader.close
     writer.close
+    logger.info("Done")
   }
 
   def minQualscore(record: VariantContext): Boolean = {
@@ -241,4 +258,9 @@ object VcfFilter extends ToolCommand {
     }
     return true
   }
+
+  def inIdSet(record: VariantContext): Boolean = {
+    if (commandArgs.iDset.isEmpty) true
+    else record.getID.split(",").exists(commandArgs.iDset.contains(_))
+  }
 }
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