Merge pull request #240 from AdamaJava/tidyup_qannotate

Tidyup qannotate

Author: ChristinaXu2017

qannotate/src/au/edu/qimr/qannotate/Main.java

@@ -20,7 +20,6 @@
 import au.edu.qimr.qannotate.modes.SnpEffMode;
 import au.edu.qimr.qannotate.modes.TandemRepeatMode;
 import au.edu.qimr.qannotate.modes.Vcf2maf;
-import au.edu.qimr.qannotate.modes.Vcf2mafTmp;
 
 public class Main {
 
@@ -57,12 +56,8 @@ public static void main(final String[] args) throws Exception {
     	   		new TandemRepeatMode( options );
             } else if (options.getMode() == Options.MODE.make_valid) {
     	   		new MakeValidMode( options );
-//           } else if (options.getMode() == Options.MODE.snppileup) {
-//   	   			new SnpPileupMode( options );
    	   	    } else if (options.getMode() == Options.MODE.overlap) {
    	   			new OverlapMode( options );
-	   	   	} else if (options.getMode() == Options.MODE.vcf2maftmp) {
-				new Vcf2mafTmp(  options );
 	   	   	} else if (options.getMode() == null) {
 	   	   		throw new IllegalArgumentException("No mode was specified on the commandline - please add the \"-mode\" option") ;
             } else {

qannotate/src/au/edu/qimr/qannotate/modes/CustomerConfidenceMode.java

@@ -15,7 +15,6 @@
 
 import au.edu.qimr.qannotate.Options;
 import au.edu.qimr.qannotate.utils.MafElement;
-import au.edu.qimr.qannotate.utils.SampleColumn;
 import au.edu.qimr.qannotate.utils.SnpEffConsequence;
 import au.edu.qimr.qannotate.utils.SnpEffMafRecord;
 
@@ -61,7 +60,7 @@ public class Vcf2maf extends AbstractMode {
 	protected final  Map<String,String> effRanking = new HashMap<>();	
 	private final String center;
 	private final String sequencer;
-	private final String donorId;	 
+ 
 	private final ContentType contentType;
 	//private boolean hasACLAP = false;	ignore ACLAP in vcf2maf mode
 	private final int testColumn;
@@ -70,7 +69,8 @@ public class Vcf2maf extends AbstractMode {
 	private  String controlSample;
 	private String testBamId;
 	private String controlBamId;
-	private int controlColumn;	
+	private String donorId;	
+	private int controlColumn;
 	private VcfFileMeta meta;
 
 	//for unit test
@@ -121,7 +121,7 @@ public Vcf2maf( Options option) throws Exception {
 			meta.getFirstControlSample().ifPresent((s) -> this.controlSample = s);
 			meta.getFirstControlBamUUID().ifPresent((s) -> this.controlBamId = s);
 			meta.getFirstTestBamUUID().ifPresent((s) -> this.testBamId = s);
-			this.donorId = option.getDonorId() == null ? SampleColumn.getDonorId(reader.getHeader()) : option.getDonorId();
+			meta.getFirstDonorID().ifPresent(s -> this.donorId = s);
 
 			logger.info(String.format("Test Sample %s is located on column %d after FORMAT", testSample, testColumn));
 			if (ContentType.multipleSamples(contentType)) {