@@ -0,0 +1,1051 @@
+package com.github.sparkcaller.preprocessing;%0A%0Aimport com.github.sparkcaller.BaseGATKProgram;%0Aimport com.github.sparkcaller.Utils;%0Aimport org.apache.spark.api.java.function.Function;%0Aimport scala.Tuple2;%0A%0Aimport java.io.File;%0Aimport java.util.ArrayList;%0A%0Apublic class IndelTargetCreator extends BaseGATKProgram implements Function%3CFile, Tuple2%3CFile, File%3E%3E %7B%0A    public IndelTargetCreator(String pathToReference, String extraArgsString) %7B%0A        super(%22RealignerTargetCreator%22, extraArgsString);%0A        setReference(pathToReference);%0A    %7D%0A%0A    public Tuple2%3CFile, File%3E call(File file) throws Exception %7B%0A        ArrayList%3CString%3E indelArgs = new ArrayList%3CString%3E();%0A%0A        setInputFile(file.getPath());%0A%0A        final String outputIntervalsFilename = Utils.removeExtenstion(file.getPath(), %22bam%22) + %22-target.intervals%22;%0A        File outputIntervalsFile = new File(outputIntervalsFilename);%0A        setOutputFile(outputIntervalsFile.getPath());%0A%0A        executeProgram();%0A        return new Tuple2%3CFile, File%3E(file, outputIntervalsFile);%0A   %7D%0A%7D%0A

Create the class used to find which intervals which requires realignment.