removed depricated python option

Author: ddecap

halvade/src/be/ugent/intec/halvade/HalvadeOptions.java

@@ -55,7 +55,6 @@ public class HalvadeOptions {
     public String ref;
     public String STARGenome = null;
     public String java = null;
-    public String python = null;
     public String gff = null;
     public String tmpDir = "/tmp/halvade/";
     public String localRefDir = null;
@@ -163,9 +162,6 @@ public int GetOptions(String[] args, Configuration hConf) throws IOException, UR
             if (java != null) {
                 HalvadeConf.setJava(hConf, java);
             }
-            if (python != null) {
-                HalvadeConf.setPython(hConf, python);
-            }
             if (gff != null) {
                 HalvadeConf.setGff(hConf, gff);
             }
@@ -378,10 +374,6 @@ protected void createOptions() {
                 .withDescription("Sets the bed file containing relevant (Exome) regions which "
                         + " will be used to filter in the GATK steps.")
                 .create("fbed");
-        Option optPython = OptionBuilder.withArgName("python")
-                .hasArg()
-                .withDescription("Sets the location of the python binary if regular python command doesn't work.")
-                .create("python");
         Option optGff = OptionBuilder.withArgName("gff")
                 .hasArg()
                 .withDescription("Sets the gff file to be used with HTSeq-Count. This is required to run HTSeq-Count.")
@@ -467,7 +459,6 @@ protected void createOptions() {
         options.addOption(optCov);
         options.addOption(optMpn);
         options.addOption(optGff);
-        options.addOption(optPython);
         options.addOption(optRpn);
         options.addOption(optDry);
         options.addOption(optDrop);
@@ -564,9 +555,6 @@ protected boolean parseArguments(String[] args, Configuration halvadeConf) throw
         if (line.hasOption("J")) {
             java = line.getOptionValue("J");
         }
-        if (line.hasOption("python")) {
-            python = line.getOptionValue("python");
-        }
         if (line.hasOption("gff")) {
             gff = line.getOptionValue("gff");
         }

halvade/src/be/ugent/intec/halvade/hadoop/mapreduce/HalvadeReducer.java

@@ -54,7 +54,6 @@ public class HalvadeReducer extends Reducer<ChromosomeRegion, SAMRecordWritable,
     protected String RGPL = "ILLUMINA";
     protected String RGPU = "UNIT1";
     protected String RGSM = "SAMPLE1";
-    protected String python;
     protected int threads;
     protected int taskNr;
     protected String referenceName;
@@ -140,7 +139,6 @@ protected void setup(Context context) throws IOException, InterruptedException {
         taskId = context.getTaskAttemptID().toString();
         taskId = taskId.substring(taskId.indexOf("r_"));
         taskNr = Integer.parseInt(taskId.split("_")[1]);
-        python = HalvadeConf.getPython(context.getConfiguration());
         outputdir = HalvadeConf.getOutDir(context.getConfiguration());
         if(inputIsBam) {
             header = SAMHeaderReader.readSAMHeaderFrom(new Path(HalvadeConf.getHeaderFile(context.getConfiguration())), context.getConfiguration());

halvade/src/be/ugent/intec/halvade/utils/HalvadeConf.java

@@ -198,14 +198,6 @@ public static void setGff(Configuration conf, String val) {
         conf.set(gff, val);       
     }
 
-    private static final String python = "python";
-    public static String getPython(Configuration conf) {
-        return conf.get(python, "python");
-    }
-    public static void setPython(Configuration conf, String val) {
-        conf.set(python, val);       
-    }
-    
     private static final String readgroup = "readgroup";
     public static void setReadGroup(Configuration conf, String val) {
         conf.set(readgroup, val);