Merge pull request #361 from AdamaJava/qsv_java21_annotate

refactor: minor java 21 refactoring of qsv packages

Author: newellf

qsv/src/org/qcmg/qsv/QSVPipeline.java

@@ -139,7 +139,7 @@ public QSVPipeline(Options options, String resultsDir, Date analysisDate, String
 		}        
 
 		if (options.isQCMG()) {
-			writeDCCHeader(options, analysisDate, analysisId, exec);
+			writeDCCHeader(options, analysisId, exec);
 		}
 
 		File countFile = new File(resultsDir + FILE_SEPARATOR + options.getSampleName()+ "_sv_counts.txt");
@@ -152,11 +152,11 @@ public QSVPipeline(Options options, String resultsDir, Date analysisDate, String
 
 	}
 
-	private void writeDCCHeader(Options options, Date analysisDate, String analysisId, QExec exec) throws IOException {
-		new DCCReport(new File(resultsDir + FILE_SEPARATOR + options.getSampleName() + ".somatic.dcc"), analysisDate, analysisId, tumor, normal, options, exec);
+	private void writeDCCHeader(Options options, String analysisId, QExec exec) throws IOException {
+		new DCCReport(new File(resultsDir + FILE_SEPARATOR + options.getSampleName() + ".somatic.dcc"), analysisId, tumor, normal, options, exec);
 		if (options.isTwoFileMode()) {
-			new DCCReport(new File(resultsDir + FILE_SEPARATOR + options.getSampleName() + ".germline.dcc"), analysisDate, analysisId, tumor, normal, options, exec);
-			new DCCReport(new File(resultsDir + FILE_SEPARATOR + options.getSampleName() + ".normal-germline.dcc"), analysisDate, analysisId, tumor, normal, options, exec);
+			new DCCReport(new File(resultsDir + FILE_SEPARATOR + options.getSampleName() + ".germline.dcc"), analysisId, tumor, normal, options, exec);
+			new DCCReport(new File(resultsDir + FILE_SEPARATOR + options.getSampleName() + ".normal-germline.dcc"), analysisId, tumor, normal, options, exec);
 		}	
 	}
 
@@ -383,11 +383,11 @@ public void annotateAndFilterBams() throws Exception {
 		CountDownLatch countDownLatch = new CountDownLatch(getThreadNo());
 
 		if (options.isTwoFileMode()) {        
-			AnnotateFilterMT normalWorker = new AnnotateFilterMT(Thread.currentThread(), countDownLatch, normal, exitStatus, softclipDir, options);        
+			AnnotateFilterMT normalWorker = new AnnotateFilterMT(countDownLatch, normal, exitStatus, softclipDir, options);
 			executorService.execute(normalWorker);
 		}
 
-		AnnotateFilterMT tumorWorker = new AnnotateFilterMT(Thread.currentThread(), countDownLatch, tumor, exitStatus, softclipDir, options);         
+		AnnotateFilterMT tumorWorker = new AnnotateFilterMT(countDownLatch, tumor, exitStatus, softclipDir, options);
 		executorService.execute(tumorWorker);
 
 		executorService.shutdown();

qsv/src/org/qcmg/qsv/annotate/AnnotateFilterMT.java

@@ -78,7 +78,7 @@ public class AnnotateFilterMT implements Runnable {
     private final boolean translocationsOnly;
 
 
-    public AnnotateFilterMT(Thread mainThread, CountDownLatch countDownLatch, QSVParameters parameters, AtomicInteger exitStatus, String softclipDir, Options options) {
+    public AnnotateFilterMT(CountDownLatch countDownLatch, QSVParameters parameters, AtomicInteger exitStatus, String softclipDir, Options options) {
         this.softClipDir = softclipDir;
         this.query = options.getPairQuery();
         this.clipQuery = options.getClipQuery();
@@ -168,8 +168,17 @@ public void run() {
             writeThreads.shutdown();
 
             logger.info("waiting for  threads to finish (max wait will be 100 hours)");
-            filterThreads.awaitTermination(Constants.EXECUTOR_SERVICE_AWAIT_TERMINATION, TimeUnit.HOURS);
-            writeThreads.awaitTermination(Constants.EXECUTOR_SERVICE_AWAIT_TERMINATION, TimeUnit.HOURS);
+
+            try {
+                if (!filterThreads.awaitTermination(Constants.EXECUTOR_SERVICE_AWAIT_TERMINATION, TimeUnit.HOURS)) {
+                    logger.error("Filtering threads did not finish within the time limit");
+                }
+                if (!writeThreads.awaitTermination(Constants.EXECUTOR_SERVICE_AWAIT_TERMINATION, TimeUnit.HOURS)) {
+                    logger.error("Writing threads did not finish within the time limit");
+                }
+            } catch (final InterruptedException e) {
+                logger.error("Thread was interrupted while waiting for executor service to terminate: " + QSVUtil.getStrackTrace(e));
+            }
 
             if (!readQueue.isEmpty() || !writeQueue.isEmpty() || !writeClipQueue.isEmpty()) {
                 throw new Exception(

qsv/src/org/qcmg/qsv/annotate/IlluminaLongMatePairRecord.java

@@ -21,7 +21,6 @@ public class IlluminaLongMatePairRecord {
     private String zpAnnotation;
     private final int isizeUpperLimit;
     private final int isizeLowerLimit;
-    private final int nullNHZ = 0;
     private int endZ = 0;
     private int sameStrandZ = 0;
 	private int diffStrandNullZ = 0;
@@ -122,11 +121,7 @@ public boolean isAbbConverted() {
 		return abbConverted;
 	}
 
-	public void setAbbConverted(boolean abbConverted) {
-		this.abbConverted = abbConverted;
-	}
-
-	/**
+    /**
 	 * Determine orientation of the record
 	 * @return current zp annotation
 	 */
@@ -318,29 +313,5 @@ public void setZPAnnotation(String zp) {
     	   this.zpAnnotation = zp;     
 
     }
-    
-    public int getNullNHZ() {
-		return nullNHZ;
-	}
-
-	public int getEndZ() {
-		return endZ;
-	}
-
-	public int getSameStrandZ() {
-		return sameStrandZ;
-	}
-
-	public int getDiffStrandNullZ() {
-		return diffStrandNullZ;
-	}
-
-	public int getDiffStrandZ() {
-		return diffStrandZ;
-	}
-
-    public int getSameStrandNullZ() {
-		return sameStrandNullZ;
-	}
 
 }

qsv/src/org/qcmg/qsv/annotate/PairingStats.java

@@ -25,13 +25,13 @@
 
 /**
  * <p>Java class for anonymous complex type.
- * 
+ *
  * <p>The following schema fragment specifies the expected content contained within this class.
- * 
+ *
  * <pre>
  * &lt;complexType>
  *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *     &lt;restriction base="{<a href="http://www.w3.org/2001/XMLSchema">...</a>}anyType">
  *       &lt;sequence>
  *         &lt;element name="InsertRange">
  *           &lt;complexType>
@@ -60,8 +60,8 @@
  *   &lt;/complexContent>
  * &lt;/complexType>
  * </pre>
- * 
- * 
+ *
+ *
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "", propOrder = {
@@ -79,7 +79,7 @@ public class PairingStats {
     protected List<PairingStats.UniquePairing> uniquePairing;
     @XmlElement(name = "ReadCount", required = true)
     protected List<PairingStats.ReadCount> readCount;
-    @XmlElement(name = "Coverage", required = false)
+    @XmlElement(name = "Coverage")
     protected List<PairingStats.Coverage> coverage;
 
     /**
@@ -151,21 +151,21 @@ public List<PairingStats.Coverage> getCoverage() {
 
     /**
      * <p>Java class for anonymous complex type.
-     * 
+     *
      * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
+     *
      * <pre>
      * &lt;complexType>
      *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *     &lt;restriction base="{<a href="http://www.w3.org/2001/XMLSchema">...</a>}anyType">
      *       &lt;attribute name="LowerLimit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
      *       &lt;attribute name="UpperLimit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
      * </pre>
-     * 
-     * 
+     *
+     *
      */
     @XmlAccessorType(XmlAccessType.FIELD)
     @XmlType(name = "")
@@ -243,13 +243,13 @@ public void setAverage(BigInteger value) {
 
     /**
      * <p>Java class for anonymous complex type.
-     * 
+     *
      * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
+     *
      * <pre>
      * &lt;complexType>
      *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *     &lt;restriction base="{<a href="http://www.w3.org/2001/XMLSchema">...</a>}anyType">
      *       &lt;sequence>
      *         &lt;element name="type" type="{http://www.w3.org/2001/XMLSchema}string"/>
      *         &lt;element name="count" type="{http://www.w3.org/2001/XMLSchema}positiveInteger"/>
@@ -258,8 +258,8 @@ public void setAverage(BigInteger value) {
      *   &lt;/complexContent>
      * &lt;/complexType>
      * </pre>
-     * 
-     * 
+     *
+     *
      */
     @XmlAccessorType(XmlAccessType.FIELD)
     @XmlType(name = "", propOrder = {

qsv/src/org/qcmg/qsv/annotate/ZPAnnotator.java

@@ -22,32 +22,32 @@ public class ZPAnnotator {
 	 * Returns a string that corresponds to the ZP annotation for the record 
 	 * (ZP=discordant pair classification)
 	 * 
-	 * NOTE that in the interests of referential transparency, this method does not set the ZP attribute in the passed in SAMREcord
+	 * NOTE that in the interests of referential transparency, this method does not set the ZP attribute in the passed in SAMRecord
 	 *  
 	 */
 	public static String createZPAnnotation(SAMRecord record, int isizeLowerLimit, int isizeUpperLimit) {
-		String zpAnnotation = "";
+		String zpAnnotation;
 		if ( ! record.getDuplicateReadFlag()) {
 
 			Integer nh = record.getIntegerAttribute(QSVConstants.NH);
 
-			if (null != nh && 1 == nh.intValue() && record.getMateUnmappedFlag()) {
+			if (null != nh && 1 == nh && record.getMateUnmappedFlag()) {
 				zpAnnotation = QSVConstants.D_STAR_STAR;
 			} else if (null != nh
-					&& 1 == nh.intValue()
+					&& 1 == nh
 					&& !record.getReferenceName().equals(
 							record.getMateReferenceName())
 					&& !record.getMateReferenceName().equals(Constants.EQ_STRING)) {
 				zpAnnotation = QSVConstants.C_STAR_STAR;
 
-			} else if (null != nh && 1 == nh.intValue()
+			} else if (null != nh && 1 == nh
 					&& record.getReadFailsVendorQualityCheckFlag()) {
 				zpAnnotation = QSVConstants.E_STAR_STAR;
 
-			} else if (null != nh && 1 == nh.intValue() && isDifferentStrand(record)) {
+			} else if (null != nh && 1 == nh && isDifferentStrand(record)) {
 				zpAnnotation = handleOrientation(record, "A");
 				zpAnnotation += handleIntervalSize(record, isizeLowerLimit, isizeUpperLimit);
-			} else if (null != nh && 1 != nh.intValue() && isDifferentStrand(record)) {
+			} else if (null != nh && 1 != nh && isDifferentStrand(record)) {
 				zpAnnotation = handleOrientation(record, "A");
 				zpAnnotation += handleIntervalSize(record, isizeLowerLimit, isizeUpperLimit);
 				if ( ! zpAnnotation.equals(QSVConstants.AAA)) {

qsv/src/org/qcmg/qsv/assemble/Alignment.java

@@ -17,16 +17,11 @@ public class Alignment {
 
 	private int start;
 	private int length;
-	
-	public Alignment(Read seed) {
-		this.seed = seed;
-		matchedReads = new ArrayList<ReadMatch>();
-	}
-	
+
 	public Alignment(ConcurrentHashMap<Integer, ReadMatch> reads, Read seed)
 	{
 		this.seed = seed;
-		matchedReads = new ArrayList<ReadMatch>(reads.values());
+		matchedReads = new ArrayList<>(reads.values());
 	}
 
 	/*
@@ -77,22 +72,22 @@ private char getConsensusBase(int position)
 		int t = 0;
 		int c = 0;
 		int g = 0;
-		for (int i = 0 , len = bases.length ; i < len ; i++) {
-			switch (bases[i]) {
-			case 'A': 
-				a++;
-				break;
-			case 'T':
-				t++;
-				break;
-			case 'C':
-				c++;
-				break;
-			case 'G':
-				g++;
-				break;
-			}
-		}
+        for (char basis : bases) {
+            switch (basis) {
+                case 'A':
+                    a++;
+                    break;
+                case 'T':
+                    t++;
+                    break;
+                case 'C':
+                    c++;
+                    break;
+                case 'G':
+                    g++;
+                    break;
+            }
+        }
 
 		if(a > t && a > c && a > g && a >= QSVAssemble.MINIMUM_READ_EXTEND) { //Is A the most common?
 			return 'A';