UMIIteratorBuilder

broadinstitute · Jul 3, 2024 · 139bc61 · 139bc61
1 parent 3df3e34
commit 139bc61
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Showing 11 changed files with 132 additions and 97 deletions.
diff --git a/src/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpression.java b/src/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpression.java
@@ -186,10 +186,10 @@ private void digitalExpression(List<String> cellBarcodes) {
 			writeDgeHeader(out);
 
         // TODO should the ambiguous reads handling be a parameter?  It's set to false by default for DGE to get rid of ambiguous gene assignments on reads
-        UMIIterator realUMIIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(Collections.singletonList(this.INPUT), false),
+        UMIIterator realUMIIterator = new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(Collections.singletonList(this.INPUT), false),
                 GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG, this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.FUNCTIONAL_STRATEGY,
-                this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG, this.READ_MQ, false, cellBarcodes,
-                false, OMIT_MISSING_CELLS);
+                this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG, this.READ_MQ).setCellBarcodes(cellBarcodes).
+                recordCellsInInput(OMIT_MISSING_CELLS).build();
         CloseableIterator<UMICollection> umiIterator = realUMIIterator;
 
         if (OMIT_MISSING_CELLS) {

diff --git a/...java/org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.java b/...java/org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.java
@@ -96,10 +96,10 @@ protected int doWork() {
                 this.CELL_BC_FILE, this.READ_MQ, this.MIN_NUM_TRANSCRIPTS_PER_CELL,
                 this.MIN_NUM_GENES_PER_CELL, this.MIN_NUM_READS_PER_CELL, this.NUM_CORE_BARCODES, this.EDIT_DISTANCE, this.MIN_BC_READ_THRESHOLD));
 
-		UMIIterator umiIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(this.INPUT, false),
+		UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(this.INPUT, false),
 				GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
         		this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.FUNCTIONAL_STRATEGY, this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
-        		this.READ_MQ, false, cellBarcodes, true, false);
+        		this.READ_MQ).setCellBarcodes(cellBarcodes).cellFirstSort(true).build();
 
 		UMICollection batch;
 
@@ -163,10 +163,10 @@ public ObjectCounter<String> getNumTranscriptsPerCell (final List<File> bamFile,
 		SamReaderFactory factory= SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.EAGERLY_DECODE);		
 		SamHeaderAndIterator headerIterator= SamFileMergeUtil.mergeInputs(bamFile, false, factory);
 
-		UMIIterator umiIterator = new UMIIterator(headerIterator,
+		UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(headerIterator,
 				geneNameTag, strandTag, geneFunctionTag,
 				strategy, locusFunctionList,  functionStrategy, cellBarcodeTag, molecularBarcodeTag,
-				mapQuality, false, cellBarcodes);
+				mapQuality).setCellBarcodes(cellBarcodes).build();
 
 		ObjectCounter<String> transcriptsPerCell = new ObjectCounter<>();
 

diff --git a/src/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReads.java b/src/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReads.java
@@ -46,10 +46,8 @@
 import org.broadinstitute.dropseqrna.utils.readiterators.GeneFunctionProcessor;
 import org.broadinstitute.dropseqrna.utils.readiterators.SamFileMergeUtil;
 import org.broadinstitute.dropseqrna.utils.readiterators.SamHeaderAndIterator;
-import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
 import org.broadinstitute.dropseqrna.utils.readiterators.UMIIterator;
 import picard.cmdline.StandardOptionDefinitions;
-import picard.illumina.BarcodeMetric;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -224,10 +222,10 @@ private Map<String, ChimericUmiCollection> identifyChimericsAndWriteReport(boole
         final Set<String> cellBarcodes=getCellBarcodes();       
 
         PeekableIterator<UMICollection> umiIterator = new PeekableIterator<>(
-                new UMIIterator(SamFileMergeUtil.mergeInputs(this.INPUT, false),
+                new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(this.INPUT, false),
                         GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
                         this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.FUNCTIONAL_STRATEGY, this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
-                        this.READ_MQ, false, cellBarcodes, true, false));
+                        this.READ_MQ).setCellBarcodes(cellBarcodes).cellFirstSort(true).build());
 
         // Remember {CBC, UMI, Gene} pairs to be marked chimeric
         final Map<String, ChimericUmiCollection> chimerics = new HashMap<>();

diff --git a/src/java/org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.java b/src/java/org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.java
@@ -131,9 +131,9 @@ protected int doWork() {
 			mapContainer = new SingleOrganismMapContainer(cellBarcodes);
 
         // gene/exon tags are sorted first, followed by cells
-        UMIIterator umiIterator = new UMIIterator(headerAndIterator, GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
+        UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(headerAndIterator, GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
         		this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.FUNCTIONAL_STRATEGY, this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
-        		this.READ_MQ, false, cellBarcodes);
+        		this.READ_MQ).setCellBarcodes(cellBarcodes).build();
 
 
         String gene = null;

diff --git a/...a/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/FilterReadsByUMISupport.java b/...a/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/FilterReadsByUMISupport.java
@@ -86,9 +86,9 @@ protected int doWork() {
 
     	FilteredUmiMetrics metrics = new FilteredUmiMetrics();
 
-    	UMIIterator umiIterator = new UMIIterator(headerAndIter,GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG, 
+    	UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(headerAndIter,GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
     			this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.FUNCTIONAL_STRATEGY, this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
-    			this.READ_MQ, false, cellBarcodes, false, false, true, null);
+    			this.READ_MQ).setCellBarcodes(cellBarcodes).retainReads(true).build();
 
     	while (umiIterator.hasNext()) {
     		UMICollection c = umiIterator.next();

diff --git a/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollectionFactory.java b/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollectionFactory.java
@@ -53,11 +53,11 @@ public class BiasedBarcodeCollectionFactory {
 	public UMIIterator prepareUMIIterator(final List<File> inputFiles, final String geneExonTag, final String cellBarcodeTag, final String molBCTag, final String strandTag,
 			final int readMQ, final List<String> cellBarcodes) {
 
-		return new UMIIterator(SamFileMergeUtil.mergeInputs(inputFiles, false, samReaderFactory),
+		return new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(inputFiles, false, samReaderFactory),
 				GeneFunctionCommandLineBase.DEFAULT_GENE_NAME_TAG, GeneFunctionCommandLineBase.DEFAULT_GENE_STRAND_TAG,
 				GeneFunctionCommandLineBase.DEFAULT_GENE_FUNCTION_TAG, GeneFunctionCommandLineBase.DEFAULT_STRAND_STRATEGY,
 				GeneFunctionCommandLineBase.DEFAULT_LOCUS_FUNCTION_LIST, GeneFunctionCommandLineBase.DEFAULT_FUNCTIONAL_STRATEGY,
-				cellBarcodeTag, molBCTag, readMQ, false, cellBarcodes, true, false);
+				cellBarcodeTag, molBCTag, readMQ).setCellBarcodes(cellBarcodes).cellFirstSort(true).build();
 
 	}
 

diff --git a/src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.java b/src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.java
@@ -588,10 +588,10 @@ public String fixUMI (final String cellBarcode, final String umi, final int erro
 	public UMIIterator prepareUMIIterator() {
 		List<String> barcodes=getCellBarcodes();
 
-		UMIIterator umiIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(INPUT, false, samReaderFactory),
+		UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(INPUT, false, samReaderFactory),
 				GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
         		this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.FUNCTIONAL_STRATEGY, this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
-        		this.READ_MQ, false, barcodes, true, false);
+        		this.READ_MQ).setCellBarcodes(barcodes).cellFirstSort(true).build();
 
 				return (umiIterator);
 	}

diff --git a/src/java/org/broadinstitute/dropseqrna/utils/editdistance/DetectBeadSubstitutionErrors.java b/src/java/org/broadinstitute/dropseqrna/utils/editdistance/DetectBeadSubstitutionErrors.java
@@ -140,12 +140,12 @@ protected int doWork() {
 
         // build up the UMI per cell data set.
         Collection <String> cellBarcodes = null;
-        UMIIterator umiIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(this.INPUT, false),
+        UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(this.INPUT, false),
 				GeneFunctionCommandLineBase.DEFAULT_GENE_NAME_TAG, GeneFunctionCommandLineBase.DEFAULT_GENE_STRAND_TAG,
                 GeneFunctionCommandLineBase.DEFAULT_GENE_FUNCTION_TAG, GeneFunctionCommandLineBase.DEFAULT_STRAND_STRATEGY,
                 GeneFunctionCommandLineBase.DEFAULT_LOCUS_FUNCTION_LIST, GeneFunctionCommandLineBase.DEFAULT_FUNCTIONAL_STRATEGY,
 				this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
-                this.READ_MQ, false, cellBarcodes, true, false);
+                this.READ_MQ).setCellBarcodes(cellBarcodes).cellFirstSort(true).build();
 
         // get list of barcodes that have enough UMIs, and are not polyT biased.
         UMIsPerCellResult umiResult=getUMIsPerCell(umiIterator, this.MIN_UMIS_PER_CELL, this.UMI_BIAS_BASE, this.UMI_BIAS_THRESHOLD, null);

diff --git a/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.java b/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.java
@@ -49,72 +49,7 @@ public class UMIIterator implements CloseableIterator<UMICollection>  {
     private final StringInterner stringCache = new StringInterner();
     private final Set<String> cellBarcodesSeen;
     private final boolean retainReads;
-	/**
-	 * Construct an object that generates UMI objects from a BAM file
-     * @param headerAndIterator The BAM records to extract UMIs from
-	 * @param geneTag The gene tag on BAM records
-	 * @param cellBarcodeTag The cell barcode tag on BAM records
-	 * @param molecularBarcodeTag The molecular barcode tag on BAM records
-	 * @param geneStrandTag The strand tag on BAM records
-	 * @param readMQ The minimum map quality of the reads
-	 * @param assignReadsToAllGenes Should records tagged with multiple genes be double counted, once for each gene?
-	 * @param strandStrategy should the gene and read strand match for the read to be accepted
-	 * @param cellBarcodes The list of cell barcode tag values that match the <cellBarcodeTag> tag on the BAM records.
-     *                     Only reads with these values will be used.  If set to null, all cell barcodes are used.
-	 */
-	public UMIIterator(final SamHeaderAndIterator headerAndIterator,
-                       final String geneTag,
-                       final String geneStrandTag,
-                       final String geneFunctionTag,
-                       final StrandStrategy strandStrategy,
-                       final Collection <LocusFunction> acceptedLociFunctions,
-					   FunctionalDataProcessorStrategy functionStrategy,
-                       final String cellBarcodeTag,
-                       final String molecularBarcodeTag,
-                       final int readMQ,
-                       final boolean assignReadsToAllGenes,
-                       final Collection<String> cellBarcodes) {
-		this(headerAndIterator, geneTag, geneStrandTag, geneFunctionTag, strandStrategy, acceptedLociFunctions, functionStrategy,
-				cellBarcodeTag, molecularBarcodeTag, readMQ, assignReadsToAllGenes, cellBarcodes, false, false);
-	}
 
-	/**
-	 * Construct an object that generates UMI objects from a BAM file
-	 * @param headerAndIterator The BAM records to extract UMIs from
-	 * @param geneTag The geneExon tag on BAM records
-	 * @param cellBarcodeTag The cell barcode tag on BAM records
-	 * @param molecularBarcodeTag The molecular barcode tag on BAM records
-	 * @param geneStrandTag The strand tag on BAM records
-	 * @param readMQ The minimum map quality of the reads
-	 * @param assignReadsToAllGenes Should records tagged with multiple genes be double counted, once for each gene?
-	 * @param strandStrategy should the gene and read strand match for the read to be accepted
-	 * @param cellBarcodes The list of cell barcode tag values that match the <cellBarcodeTag> tag on the BAM records.
-     *                     Only reads with these values will be used.  If set to null, all cell barcodes are used.
-	 * @param cellFirstSort if true, then cell barcodes are sorted first, followed by gene/exon tags.
-     *                      If false, then gene/exon tags are sorted first, followed by cells.  false is the default and used in the other constructor.
-	 * @param recordCellsInInput While sorting the input, keep track of what cells appear in the input.  This record
-	 *                           is not complete until iteration is started.
-	 */
-	public UMIIterator(final SamHeaderAndIterator headerAndIterator,
-					   final String geneTag,
-                       final String geneStrandTag,
-                       final String geneFunctionTag,
-                       final StrandStrategy strandStrategy,
-                       final Collection <LocusFunction> acceptedLociFunctions,
-					   FunctionalDataProcessorStrategy functionStrategy,
-                       final String cellBarcodeTag,
-                       final String molecularBarcodeTag,
-                       final int readMQ,
-                       final boolean assignReadsToAllGenes,
-                       final Collection<String> cellBarcodes,
-                       final boolean cellFirstSort,
-					   final boolean recordCellsInInput) {
-
-		this(headerAndIterator, geneTag, geneStrandTag, geneFunctionTag, strandStrategy, acceptedLociFunctions, functionStrategy,
-				cellBarcodeTag, molecularBarcodeTag, readMQ, assignReadsToAllGenes, cellBarcodes, cellFirstSort, recordCellsInInput, false,
-				null);
-
-	}
 	/**
 	 * Construct an object that generates UMI objects from a BAM file
 	 * @param headerAndIterator The BAM records to extract UMIs from
@@ -135,7 +70,7 @@ public UMIIterator(final SamHeaderAndIterator headerAndIterator,
 	 * This is false in other method signatures by default.  If false, reads can be simplified for faster serialization.
 	 * 
 	 */
-	public UMIIterator(final SamHeaderAndIterator headerAndIterator,
+	private UMIIterator(final SamHeaderAndIterator headerAndIterator,
 					   final String geneTag,
                        final String geneStrandTag,
                        final String geneFunctionTag,
@@ -376,4 +311,105 @@ public int compare(SAMRecord o1, SAMRecord o2) {
 			return comp.fileOrderCompare(o1, o2);
 		}
 	}
+
+	public static class UMIIteratorBuilder {
+		// required parameters
+		private final SamHeaderAndIterator headerAndIterator;
+		private final String geneTag;
+		private final String geneStrandTag;
+		private final String geneFunctionTag;
+		private final StrandStrategy strandStrategy;
+		private final Collection <LocusFunction> acceptedLociFunctions;
+		private final FunctionalDataProcessorStrategy functionStrategy;
+		private final String cellBarcodeTag;
+		private final String molecularBarcodeTag;
+		private final int readMQ;
+
+		// parameters with default values
+		private boolean assignReadsToAllGenes=false;
+		private boolean cellFirstSort=false;
+		private boolean recordCellsInInput=false;
+		private boolean retainReads=false;
+
+		// nullable parameters
+		private Collection<String> cellBarcodes;
+		private IntervalList intervals;
+
+		public UMIIteratorBuilder(SamHeaderAndIterator headerAndIterator, String geneTag, String geneStrandTag,
+								  String geneFunctionTag, StrandStrategy strandStrategy,
+								  Collection<LocusFunction> acceptedLociFunctions,
+								  FunctionalDataProcessorStrategy functionStrategy, String cellBarcodeTag,
+								  String molecularBarcodeTag, int readMQ) {
+			this.headerAndIterator = headerAndIterator;
+			this.geneTag = geneTag;
+			this.geneStrandTag = geneStrandTag;
+			this.geneFunctionTag = geneFunctionTag;
+			this.strandStrategy = strandStrategy;
+			this.acceptedLociFunctions = acceptedLociFunctions;
+			this.functionStrategy = functionStrategy;
+			this.cellBarcodeTag = cellBarcodeTag;
+			this.molecularBarcodeTag = molecularBarcodeTag;
+			this.readMQ = readMQ;
+		}
+
+		public boolean isAssignReadsToAllGenes() {
+			return assignReadsToAllGenes;
+		}
+
+		public UMIIteratorBuilder assignReadsToAllGenes(boolean assignReadsToAllGenes) {
+			this.assignReadsToAllGenes = assignReadsToAllGenes;
+			return this;
+		}
+
+		public boolean isCellFirstSort() {
+			return cellFirstSort;
+		}
+
+		public UMIIteratorBuilder cellFirstSort(boolean cellFirstSort) {
+			this.cellFirstSort = cellFirstSort;
+			return this;
+		}
+
+		public boolean isRecordCellsInInput() {
+			return recordCellsInInput;
+		}
+
+		public UMIIteratorBuilder recordCellsInInput(boolean recordCellsInInput) {
+			this.recordCellsInInput = recordCellsInInput;
+			return this;
+		}
+
+		public boolean isRetainReads() {
+			return retainReads;
+		}
+
+		public UMIIteratorBuilder retainReads(boolean retainReads) {
+			this.retainReads = retainReads;
+			return this;
+		}
+
+		public Collection<String> getCellBarcodes() {
+			return cellBarcodes;
+		}
+
+		public UMIIteratorBuilder setCellBarcodes(Collection<String> cellBarcodes) {
+			this.cellBarcodes = cellBarcodes;
+			return this;
+		}
+
+		public IntervalList getIntervals() {
+			return intervals;
+		}
+
+		public UMIIteratorBuilder setIntervals(IntervalList intervals) {
+			this.intervals = intervals;
+			return this;
+		}
+
+		public UMIIterator build() {
+			return new UMIIterator(headerAndIterator, geneTag, geneStrandTag, geneFunctionTag, strandStrategy,
+					acceptedLociFunctions, functionStrategy, cellBarcodeTag, molecularBarcodeTag, readMQ,
+					assignReadsToAllGenes, cellBarcodes, cellFirstSort, recordCellsInInput, retainReads, intervals);
+		}
+	}
 }
diff --git a/src/tests/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpressionTest.java b/src/tests/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpressionTest.java
@@ -73,10 +73,9 @@ public class DigitalExpressionTest {
 	private static UMIIterator getUMIIterator (final File inFile) {
 		List<String> cellBarcodes = Arrays.asList(DigitalExpressionTestUtil.barcodes);
 
-		UMIIterator umiIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(Collections.singletonList(inFile), false), GENE_NAME_TAG,
+		UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(Collections.singletonList(inFile), false), GENE_NAME_TAG,
 				GENE_STRAND_TAG, GENE_FUNCTION_TAG, STRAND_STRATEGY, LOCUS_FUNCTION_LIST, GeneFunctionCommandLineBase.DEFAULT_FUNCTIONAL_STRATEGY,
-				CELL_BARCODE_TAG, MOLECULAR_BARCODE_TAG, READ_MQ, true, cellBarcodes, false, false,
-				false, null);
+				CELL_BARCODE_TAG, MOLECULAR_BARCODE_TAG, READ_MQ).assignReadsToAllGenes(true).setCellBarcodes(cellBarcodes).build();
 
 		return (umiIterator);
 	}
@@ -202,13 +201,16 @@ public void DGEIntegrationTest () {
 		Assert.assertNotEquals(count,0);
 	}
 
+	@Test
 	public void testTwoGenesOnSameStrand () {
 		List barcodes = Collections.singletonList("FOO");
 		File inFile = new File ("");
 
-		UMIIterator umiIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(Collections.singletonList(inFile), false), GENE_NAME_TAG,
-				GENE_STRAND_TAG, GENE_FUNCTION_TAG, this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, GeneFunctionCommandLineBase.DEFAULT_FUNCTIONAL_STRATEGY,
-				this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG, this.READ_MQ, true, barcodes);
+		UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(
+				SamFileMergeUtil.mergeInputs(Collections.singletonList(inFile), false), GENE_NAME_TAG,
+				GENE_STRAND_TAG, GENE_FUNCTION_TAG, this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST,
+				GeneFunctionCommandLineBase.DEFAULT_FUNCTIONAL_STRATEGY, this.CELL_BARCODE_TAG,
+				this.MOLECULAR_BARCODE_TAG, this.READ_MQ).setAssignReadsToAllGenes(true).setCellBarcodes(barcodes).build();
 	}
 
 

diff --git a/...ests/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollectionTest.java b/...ests/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollectionTest.java
@@ -138,13 +138,12 @@ public void testDownsample() {
 	// Do UMI collapse and confirm that the UMI counts are the same as DigitalExpressionTest.doWork()
 	@Test
 	public void testEditDistanceCollapse() {
-		final UMIIterator umiIterator = new UMIIterator(SamFileMergeUtil.mergeInputs(Collections.singletonList(DigitalExpressionTestUtil.IN_FILE), false),
+		final UMIIterator umiIterator = new UMIIterator.UMIIteratorBuilder(SamFileMergeUtil.mergeInputs(Collections.singletonList(DigitalExpressionTestUtil.IN_FILE), false),
 				DigitalExpressionTest.GENE_NAME_TAG,
 				DigitalExpressionTest.GENE_STRAND_TAG, DigitalExpressionTest.GENE_FUNCTION_TAG, DigitalExpressionTest.STRAND_STRATEGY,
 				DigitalExpressionTest.LOCUS_FUNCTION_LIST, GeneFunctionCommandLineBase.DEFAULT_FUNCTIONAL_STRATEGY,
-				"XC", DigitalExpressionTest.MOLECULAR_BARCODE_TAG, DigitalExpressionTest.READ_MQ,
-				false, Arrays.asList(DigitalExpressionTestUtil.barcodes), false, false,
-				true, null);
+				"XC", DigitalExpressionTest.MOLECULAR_BARCODE_TAG, DigitalExpressionTest.READ_MQ).
+				setCellBarcodes(Arrays.asList(DigitalExpressionTestUtil.barcodes)).retainReads(true).build();
 
 		final Map<Pair<String, String>, Integer> umiCounts = new HashMap<>();
 		for (final UMICollection c : new IterableAdapter<UMICollection>(umiIterator)) {