Add option to filter UMI iterator with an IntervalList

broadinstitute · Jun 27, 2024 · 9466915 · 9466915
1 parent 1b19813
commit 9466915
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/...a/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/FilterReadsByUMISupport.java b/...a/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/FilterReadsByUMISupport.java
@@ -88,7 +88,7 @@ protected int doWork() {
 
     	UMIIterator umiIterator = new UMIIterator(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);
+    			this.READ_MQ, false, cellBarcodes, false, false, true, null);
 
     	while (umiIterator.hasNext()) {
     		UMICollection c = umiIterator.next();

diff --git a/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.java b/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.java
@@ -111,7 +111,8 @@ public UMIIterator(final SamHeaderAndIterator headerAndIterator,
 					   final boolean recordCellsInInput) {
 
 		this(headerAndIterator, geneTag, geneStrandTag, geneFunctionTag, strandStrategy, acceptedLociFunctions, functionStrategy,
-				cellBarcodeTag, molecularBarcodeTag, readMQ, assignReadsToAllGenes, cellBarcodes, cellFirstSort, recordCellsInInput, false);
+				cellBarcodeTag, molecularBarcodeTag, readMQ, assignReadsToAllGenes, cellBarcodes, cellFirstSort, recordCellsInInput, false,
+				null);
 
 	}
 	/**
@@ -148,7 +149,8 @@ public UMIIterator(final SamHeaderAndIterator headerAndIterator,
                        final Collection<String> cellBarcodes,
                        final boolean cellFirstSort,
 					   final boolean recordCellsInInput, 
-					   final boolean retainReads) {
+					   final boolean retainReads,
+					   final IntervalList intervals) {
 
 		this.retainReads=retainReads;
         this.geneTag=geneTag;
@@ -188,6 +190,9 @@ public UMIIterator(final SamHeaderAndIterator headerAndIterator,
 			filteringIterator =
 					new TagValueFilteringIterator<>(filteringIterator, this.cellBarcodeTag, cellBarcodes);
 		}
+		if (intervals != null) {
+			filteringIterator = new IntervalFilteringIterator(filteringIterator, intervals, true);
+		}
 
 		// Filter/assign reads based on functional annotations
 		GeneFunctionIteratorWrapper wrapper = new GeneFunctionIteratorWrapper(filteringIterator, geneTag,