fixed mergeBam

Author: ddecap

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

@@ -394,6 +394,10 @@ protected void createOptions() {
                 .withDescription("Adds custom arguments for a tool. If a module in a tool is used, add the name after an underscore. "
                         + "Possible values: " + getProgramNames())
                 .create("CA");
+        Option optVerbose = OptionBuilder.withArgName("num")
+                .hasArg()
+                .withDescription("Sets verbosity of debugging [2].")
+                .create("v");
         Option optAln = OptionBuilder.withArgName("num")
                 .hasArg()
                 .withDescription("Sets the aligner used in Halvade. Possible values are 0 (bwa aln+sampe)[default], 1 (bwa mem), 2 (bowtie2), 3 (cushaw2).")
@@ -474,6 +478,7 @@ protected void createOptions() {
         options.addOption(optRedis);
         options.addOption(optRmem);
         options.addOption(optMergeBam);
+        options.addOption(optVerbose);
     }
 
     protected boolean parseArguments(String[] args, Configuration halvadeConf) throws ParseException {
@@ -609,6 +614,9 @@ protected boolean parseArguments(String[] args, Configuration halvadeConf) throw
         if (line.hasOption("fbed")) {
             filterBed = line.getOptionValue("fbed");
         }
+        if (line.hasOption("v")) {
+            Logger.SETLEVEL(Integer.parseInt(line.getOptionValue("v")));
+        }
 
         if (line.hasOption("CA")) {
             Properties props = line.getOptionProperties("CA");

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

@@ -182,7 +182,7 @@ protected int runHalvadeJob(Configuration halvadeConf, String tmpOutDir, int job
             halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.RnaGATKReducer.class);
         } else if(jobType == HalvadeResourceManager.DNA){ 
             halvadeJob.setMapperClass(halvadeOpts.alignmentTools[halvadeOpts.aln]);
-            halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.DnaGATKReducer.class);  
+            halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.DnaGATKReducer.class);
         }
 
 

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

@@ -6,6 +6,7 @@
 
 package be.ugent.intec.halvade.hadoop.mapreduce;
 
+import be.ugent.intec.halvade.hadoop.datatypes.ChromosomeRegion;
 import be.ugent.intec.halvade.utils.HalvadeConf;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMReadGroupRecord;
@@ -25,19 +26,20 @@
  *
  * @author ddecap
  */
-public class BamMergeReducer extends Reducer<LongWritable, SAMRecordWritable, LongWritable, SAMRecordWritable> {
+public class BamMergeReducer extends Reducer<ChromosomeRegion, SAMRecordWritable, LongWritable, SAMRecordWritable> {
 
     protected SAMFileHeader header;
     protected SAMSequenceDictionary dict;
-    KeyIgnoringBAMOutputFormat outpFormat;
+    protected KeyIgnoringBAMOutputFormat outpFormat;
     protected String RGID = "GROUP1";    
     protected String RGLB = "LIB1";
     protected String RGPL = "ILLUMINA";
     protected String RGPU = "UNIT1";
     protected String RGSM = "SAMPLE1";
     protected SAMReadGroupRecord bamrg;
     protected boolean inputIsBam = false;
-    RecordWriter<LongWritable,SAMRecordWritable> recordWriter;
+    protected RecordWriter<LongWritable,SAMRecordWritable> recordWriter;
+    protected LongWritable outKey;
     boolean reportBest = false;
 
     @Override
@@ -47,17 +49,18 @@ public void run(Context context) throws IOException, InterruptedException {
     }
 
     @Override
-    protected void reduce(LongWritable key, Iterable<SAMRecordWritable> values, Context context) throws IOException, InterruptedException {
+    protected void reduce(ChromosomeRegion key, Iterable<SAMRecordWritable> values, Context context) throws IOException, InterruptedException {
         Iterator<SAMRecordWritable> it = values.iterator();
         while(it.hasNext())
-            recordWriter.write(key, it.next());
+            recordWriter.write(outKey, it.next());
     }
 
     @Override
     protected void setup(Context context) throws IOException, InterruptedException {
         outpFormat = new KeyIgnoringBAMOutputFormat();
         String output = HalvadeConf.getOutDir(context.getConfiguration());
         inputIsBam = HalvadeConf.inputIsBam(context.getConfiguration());
+        dict = HalvadeConf.getSequenceDictionary(context.getConfiguration());
         if(inputIsBam) {
             header = SAMHeaderReader.readSAMHeaderFrom(new Path(HalvadeConf.getHeaderFile(context.getConfiguration())), context.getConfiguration());
         } else {
@@ -74,6 +77,8 @@ protected void setup(Context context) throws IOException, InterruptedException {
 
         outpFormat.setSAMHeader(header);
         recordWriter = outpFormat.getRecordWriter(context, new Path(output + "mergedBam.bam"));
+        outKey = new LongWritable();
+        outKey.set(0);
     }
 
         protected void getReadGroupData(Configuration conf) {

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

@@ -255,7 +255,7 @@ private void calculateRegionsPerChromosome(String bedFile) throws IOException {
                 for (BedRegion breg : region.getValue()) {
                     regionCount++;
                     Logger.DEBUG("region: " + breg.key + ", " + contig + 
-                            " (" + breg.start + " _ " + breg.end + " -> " + (breg.end - breg.start) + ")", 2);
+                            " (" + breg.start + " _ " + breg.end + " -> " + (breg.end - breg.start) + ")", 3);
                 }
             }                    
         } finally {