Removed support for representing tandem duplications as negative CIGA…

…R elements due to API change in htsjdk

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>1.5.0-SNAPSHOT</version>
+	<version>1.5.0</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>

src/main/java/au/edu/wehi/idsv/AssemblyFactory.java

@@ -160,14 +160,14 @@ private static SAMRecord createAssemblySAMRecord(
 					c.add(new CigarElement(insSize, CigarOperator.INSERTION));
 				}
 				if (delSize != 0) {
-					c.add(new CigarElement(delSize, CigarOperator.DELETION));
 					if (delSize < 0) {
 						if (!MessageThrottler.Current.shouldSupress(log, "negative deletion")) {
 							log.warn("Negative deletions not supported by SAM specs. Breakpoint assembly has been converted to breakend. "
 									+ "Sanity check failure: this should not be possible for positional assembly. ");
 						}
 						return createAssemblySAMRecord(processContext, assemblyIdGenerator, evidence, samFileHeader, source, bp.localBreakend(), startAnchoredBaseCount, 0, baseCalls, baseQuals);
 					}
+					c.add(new CigarElement(delSize, CigarOperator.DELETION));
 				}
 				c.add(new CigarElement(endAnchoredBaseCount, CigarOperator.MATCH_OR_MISMATCH));
 				record.setCigar(new Cigar(c));
@@ -199,12 +199,13 @@ private static void truncateAnchorToContigBounds(ProcessingContext processContex
 		if (r.getAlignmentStart() < 1) {
 			int basesToTruncate = 1 - r.getAlignmentStart();
 			ArrayList<CigarElement> cigar = new ArrayList<>(r.getCigar().getCigarElements());
-			cigar.set(0, new CigarElement(cigar.get(0).getLength() - basesToTruncate, cigar.get(0).getOperator()));
-			if (cigar.get(0).getLength() < 0) {
+			int len = cigar.get(0).getLength() - basesToTruncate;
+			if (len < 0) {
 				if (!MessageThrottler.Current.shouldSupress(log, "truncating assembly to contig bounds")) {
 					log.warn(String.format("Attempted to truncate %d bases from start of %s with CIGAR %s", basesToTruncate, r.getReadName(), r.getCigarString()));
 				}
 			} else {
+				cigar.set(0, new CigarElement(len, cigar.get(0).getOperator()));
 				r.setAlignmentStart(1);
 				r.setCigar(new Cigar(cigar));
 				byte[] b = r.getReadBases();
@@ -221,12 +222,13 @@ private static void truncateAnchorToContigBounds(ProcessingContext processContex
 			int basesToTruncate = r.getAlignmentEnd() - end;
 			ArrayList<CigarElement> cigar = new ArrayList<>(r.getCigar().getCigarElements());
 			CigarElement ce = cigar.get(cigar.size() - 1);
-			ce = new CigarElement(ce.getLength() - basesToTruncate, ce.getOperator());
-			if (ce.getLength() < 1) {
+			int len = ce.getLength() - basesToTruncate;
+			if (len < 1) {
 				if (!MessageThrottler.Current.shouldSupress(log, "truncating assembly to contig bounds")) {
 					log.warn(String.format("Attempted to truncate %d bases from end of %s with CIGAR %s", basesToTruncate, r.getReadName(), r.getCigarString()));
 				}
 			} else {
+				ce = new CigarElement(len, ce.getOperator());
 				cigar.set(cigar.size() - 1, ce);
 				r.setCigar(new Cigar(cigar));
 				byte[] b = r.getReadBases();

src/test/java/au/edu/wehi/idsv/Manual.java

@@ -10,7 +10,6 @@
 
 import org.apache.commons.configuration.ConfigurationException;
 import org.junit.Assert;
-import org.junit.Test;
 import org.junit.experimental.categories.Category;
 
 import au.edu.wehi.idsv.configuration.GridssConfiguration;

src/test/java/au/edu/wehi/idsv/debruijn/positional/KmerEvidenceTest.java

@@ -306,7 +306,7 @@ public void readpair_breakpoint_contig_bounds_truncation_should_not_affect_kmer_
 		assertEquals(-3, e.endPosition());
 	}
 	@Test(expected=NotImplementedException.class)
-	public void does_not_handling_XNX_unanchored_clips() {
+	public void does_not_handle_XNX_unanchored_clips() {
 		KmerEvidence.create(2, SCE(BWD, Read(0, 1, "10S1X10N1X")));
 	}
 	@Test

src/test/java/au/edu/wehi/idsv/sam/CigarUtilTest.java

@@ -12,7 +12,6 @@
 import org.apache.commons.lang3.tuple.Pair;
 import org.junit.Test;
 
-import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
 
 import htsjdk.samtools.Cigar;
@@ -120,12 +119,7 @@ public void commonReferenceBases_should_count_common() {
 	}
 	@Test
 	public void commonReferenceBases_should_match_unencoded_and_decoded_negative_deletions() {
-		Cigar c1 = new Cigar(ImmutableList.of(
-				new CigarElement(2, CigarOperator.M),
-				new CigarElement(-2, CigarOperator.D),
-				new CigarElement(2, CigarOperator.M)
-				));
-		assertEquals(4, CigarUtil.commonReferenceBases(c1, new Cigar(C("2M5P5N5P2M"))));
+		assertEquals(4, CigarUtil.commonReferenceBases(new Cigar(C("2M5D2M")), new Cigar(C("2M2D2M"))));
 	}
 	//@Test
 	public void test_realign_anchor_direction_changing_na12878() throws IOException {