Improved QueryInterval log messages

PapenfussLab · Dec 30, 2016 · 8d0b44f · 8d0b44f
1 parent 2d6b544
commit 8d0b44f
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/src/main/java/au/edu/wehi/idsv/AssemblyEvidenceSource.java b/src/main/java/au/edu/wehi/idsv/AssemblyEvidenceSource.java
@@ -243,7 +243,7 @@ private void assembleChunk(SAMFileWriter writer, SAMFileWriter filteredWriter, Q
 		}
 	}
 	private void loadAssemblyEvidenceAllocation(GreedyAssemblyAllocationCache cache, File in, QueryInterval qi) throws IOException {
-		log.debug("Caching assembly evidence allocation in interval " + qi.toString());
+		log.debug(String.format("Caching assembly evidence allocation in interval %s:%d-%d", getContext().getDictionary().getSequence(qi.referenceIndex).getSequenceName(), qi.start, qi.end));
 		QueryInterval expanded = getExpanded(qi);
 		try (CloseableIterator<DirectedEvidence> reads = mergedIterator(source, expanded)) {
 			try (SamReader reader = factory.open(in)) {
@@ -267,7 +267,7 @@ private void loadAssemblyEvidenceAllocation(GreedyAssemblyAllocationCache cache,
 		}
 	}
 	private void deduplicateChunk(File in, File out, QueryInterval qi, GreedyAssemblyAllocationCache cache) throws IOException {
-		log.debug("Uniquely assigning assembly evidence allocation in interval " + qi.toString());
+		log.debug(String.format("Uniquely assigning assembly evidence allocation in interval %s:%d-%d", getContext().getDictionary().getSequence(qi.referenceIndex).getSequenceName(), qi.start, qi.end));
 		File tmpout = FileSystemContext.getWorkingFileFor(out);
 		QueryInterval expanded = getExpanded(qi);
 		try (CloseableIterator<DirectedEvidence> reads = mergedIterator(source, expanded)) {

diff --git a/src/test/java/au/edu/wehi/idsv/SingleReadEvidenceTest.java b/src/test/java/au/edu/wehi/idsv/SingleReadEvidenceTest.java
@@ -9,7 +9,6 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.Map.Entry;
-import java.util.stream.Collector;
 import java.util.stream.Collectors;
 
 import org.junit.Test;