Initial BAM View changes to fix selection issues, zooming into secondary...

Initial BAM View changes to fix selection issues, zooming into secondary alignments, erroneous collapsing of reads with same start/end position and display of SNPs - related to RT ticket 597652

test/build-test.xml

@@ -350,6 +350,9 @@
 				<jvmarg value="-Djava.awt.headless=true" />
 				<batchtest fork="yes" todir="${junit.reports.dir}">
 					<fileset dir="${evosuite.tests.src.dir}">
+						
+						<!--include name="**/*BamView_ESTest.java" if="${do.run.evosuite.tests}" /-->
+						
 						<include name="**/*_ESTest.java" if="${do.run.evosuite.tests}" />
 						
 						<!-- Exclude classes that currently produce broken tests -->
@@ -382,7 +385,7 @@
 	</target>
 	
 	<!-- Create Jacoco reports -->
-	<target name="jacoco-coverage-report">
+	<target name="jacoco-coverage-report" depends="run-manual-tests">
 
 		<delete dir="${coverage.report.jacoco.dir}" />
 		<mkdir dir="${coverage.report.jacoco.dir}" />

uk/ac/sanger/artemis/components/alignment/BamUtils.java

@@ -362,5 +362,28 @@ class BamUtils
     }
     return featureReadCount;
   }
+  
+  /**
+   * Check whether two SAM records are the same.
+   * @param bamRec1 SamViewRecord
+   * @param bamRec2 SamViewRecord
+   * @return boolean - true if equality holds.
+   */
+  public static boolean samRecordEqualityCheck(SAMRecord rec1, SAMRecord rec2)
+  {
+	  boolean result = false;
+	  
+	  if (rec1 == null && rec2 == null)
+		  return true;
+	  
+	  result = (
+		(rec1.getReadName().equals(rec2.getReadName())) &&
+		(rec1.getAlignmentStart() == rec2.getAlignmentStart()) &&
+		(rec1.getAlignmentEnd() == rec2.getAlignmentEnd()) &&
+		(rec1.getFlags() == rec2.getFlags())
+	  );
+	  
+	  return result;
+  }
 }
 

uk/ac/sanger/artemis/components/alignment/SAMRecordSequenceString.java

+package uk.ac.sanger.artemis.components.alignment;
+
+/**
+ * Utility class that handles operations on an alignment block
+ * string taking into account the possibility that it could be
+ * a secondary alignment.
+ * 
+ * @author kp11
+ *
+ */
+public class SAMRecordSequenceString 
+{
+
+	public final static char SECONDARY_ALIGNMENT_BASE_CHAR = '=';
+	public final static char SECONDARY_ALIGNMENT_MARKER = '*';
+	
+	private String sequence;
+	private boolean isSecondaryAlignment;
+	
+	public SAMRecordSequenceString(String sequence) 
+	{
+		this.sequence = sequence;
+		this.isSecondaryAlignment = (String.valueOf(SECONDARY_ALIGNMENT_MARKER).equals(sequence));
+	}
+
+	public String substring(int beginIdx, int endIdx) 
+	{
+		
+		String result = null;
+		
+		if (!isSecondaryAlignment()) 
+		{
+			result = sequence.substring(beginIdx, endIdx);
+		} 
+		else
+		{
+			result =  new String(new char[endIdx-beginIdx]).replace('\0', SECONDARY_ALIGNMENT_BASE_CHAR);
+		}
+		
+		return result;
+
+	}
+	
+	public char charAt(int idx) 
+	{
+		
+		char result;
+		
+		if (!isSecondaryAlignment()) 
+		{
+			result = sequence.charAt(idx);
+		}
+		else
+		{
+			result = SECONDARY_ALIGNMENT_BASE_CHAR;
+		}
+		
+		return result;
+	}
+
+	public String getSequence() 
+	{
+		return sequence;
+	}
+	
+	public int length() 
+	{
+		return sequence.length();
+	}
+	
+	public boolean isSecondaryAlignment() {
+		return isSecondaryAlignment;
+	}
+}