Filter reads that STARsolo has marked as chimeric

src/java/org/broadinstitute/dropseqrna/barnyard/digitalallelecounts/SNPUMIBasePileupIterator.java

@@ -38,13 +38,7 @@
 import org.broadinstitute.dropseqrna.utils.ProgressLoggingIterator;
 import org.broadinstitute.dropseqrna.utils.SamWriterSink;
 import org.broadinstitute.dropseqrna.utils.StringTagComparator;
-import org.broadinstitute.dropseqrna.utils.readiterators.ChromosomeFilteringIterator;
-import org.broadinstitute.dropseqrna.utils.readiterators.GeneFunctionIteratorWrapper;
-import org.broadinstitute.dropseqrna.utils.readiterators.MapQualityFilteredIterator;
-import org.broadinstitute.dropseqrna.utils.readiterators.MissingTagFilteringIterator;
-import org.broadinstitute.dropseqrna.utils.readiterators.SamHeaderAndIterator;
-import org.broadinstitute.dropseqrna.utils.readiterators.SamRecordSortingIteratorFactory;
-import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
+import org.broadinstitute.dropseqrna.utils.readiterators.*;
 
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceDictionary;
@@ -103,11 +97,12 @@ public SNPUMIBasePileupIterator (final SamHeaderAndIterator headerAndIter, final
 		final ProgressLogger logger = new ProgressLogger(LOG);
 
         // add a progress logger.
-        ProgressLoggingIterator loggingIterator = new ProgressLoggingIterator (headerAndIter.iterator, logger);
+        final ProgressLoggingIterator loggingIterator = new ProgressLoggingIterator (headerAndIter.iterator, logger);
+		final STARSoloChimericReadFilteringIterator chimericReadFilteringIterator = new STARSoloChimericReadFilteringIterator(loggingIterator, molecularBarcodeTag);
 
         // filter out to contigs in the interval list.
         Set<String> contigsToFilter = snpIntervals.getIntervals().stream().map(x -> x.getContig()).collect(Collectors.toSet());
-        ChromosomeFilteringIterator cfi = new ChromosomeFilteringIterator(loggingIterator, contigsToFilter, false);
+        ChromosomeFilteringIterator cfi = new ChromosomeFilteringIterator(chimericReadFilteringIterator, contigsToFilter, false);
 
         // Filter reads on map quality
      	MapQualityFilteredIterator filteringIterator = new MapQualityFilteredIterator(cfi, readMQ, true);

src/java/org/broadinstitute/dropseqrna/utils/readiterators/STARSoloChimericReadFilteringIterator.java

@@ -0,0 +1,57 @@
+/*
+ * MIT License
+ *
+ * Copyright 2024 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+package org.broadinstitute.dropseqrna.utils.readiterators;
+
+import htsjdk.samtools.SAMRecord;
+import org.broadinstitute.dropseqrna.utils.FilteredIterator;
+
+import java.util.Iterator;
+
+/**
+ * Filter out reads that STARsolo has marked as chimeric.
+ */
+public class STARSoloChimericReadFilteringIterator
+        extends FilteredIterator<SAMRecord> {
+
+    private final String molecularBarcodeTag;
+
+    public STARSoloChimericReadFilteringIterator(Iterator<SAMRecord> underlyingIterator, String molecularBarcodeTag) {
+        super(underlyingIterator);
+        this.molecularBarcodeTag = molecularBarcodeTag;
+    }
+
+    @Override
+    public boolean filterOut(SAMRecord rec) {
+        final String umi = rec.getStringAttribute(molecularBarcodeTag);
+        if (umi == null) {
+            throw new IllegalArgumentException("Read " + rec.getSAMString() + " does not have a UMI tag " + molecularBarcodeTag);
+        }
+        return umi.equals(CHIMERIC_UMI);
+    }
+
+    /**
+     * The UMI value that STARsolo uses to indicate a chimeric read.
+     */
+    public static final String CHIMERIC_UMI = "-";
+}

src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.java

@@ -166,6 +166,9 @@ public UMIIterator(final SamHeaderAndIterator headerAndIterator,
 		Iterator<SAMRecord> filteringIterator =
                 new MissingTagFilteringIterator(headerAndIterator.iterator, cellBarcodeTag, geneTag, molecularBarcodeTag);
 
+		// Filter out reads that STARsolo has marked as chimeric
+		filteringIterator = new STARSoloChimericReadFilteringIterator(filteringIterator, molecularBarcodeTag);
+
 		// Filter reads on map quality.  Optionally keep non-primary reads at low map quality.
 		boolean rejectNonPrimaryReads = readMQ>3;
 		if (!rejectNonPrimaryReads)

src/tests/java/org/broadinstitute/dropseqrna/utils/readiterators/STARSoloChimericReadFilteringIteratorTest.java

@@ -0,0 +1,50 @@
+/*
+ * MIT License
+ *
+ * Copyright 2024 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+package org.broadinstitute.dropseqrna.utils.readiterators;
+
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+public class STARSoloChimericReadFilteringIteratorTest {
+
+ public final File INPUT = new File("testdata/org/broadinstitute/dropseq/utils/readiterators/STARsolo_chimeric_marked.sam");
+
+ @Test
+ public void testBasic() {
+  SamReader reader = SamReaderFactory.makeDefault().open(INPUT);
+  STARSoloChimericReadFilteringIterator iterator = new STARSoloChimericReadFilteringIterator(reader.iterator(), "XM");
+  int numPassing = 0;
+    while (iterator.hasNext()) {
+     ++numPassing;
+     final SAMRecord rec = iterator.next();
+     Assert.assertEquals(rec.getReadName(), "not_chimeric");
+    }
+    Assert.assertEquals(numPassing, 1);
+ }
+}

testdata/org/broadinstitute/dropseq/utils/readiterators/STARsolo_chimeric_marked.sam

@@ -0,0 +1,5 @@
+@HD	VN:1.5	SO:coordinate
+@SQ	SN:1	LN:249250621	M5:1b22b98cdeb4a9304cb5d48026a85128	UR:file:/broad/mccarroll/software/metadata/individual_reference/hg19/hg19.fasta
+@RG	ID:00000.1	SM:N701	LB:N701	PL:illumina	PU:000000000-AMY9M.1.TAAGGCGA	CN:BI	DT:2016-02-02T00:00:00-0500
+not_chimeric	0	1	564475	3	50M	*	0	0	CTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATT	AAAB3FF5DF4BEGFGGFGGFGHCHGHGGCEEGEG?FEGEFHHGGGGEHH	XC:Z:CGCCTCCTCCGA	MD:Z:50	XF:Z:INTERGENIC	PG:Z:STAR	RG:Z:00000.1	XG:Z:RP5-857K21.4	NH:i:2	NM:i:0	XM:Z:TTTCTGTG	UQ:i:0	AS:i:49	gf:Z:INTRONIC	gn:Z:RP5-857K21.4	gs:Z:-
+chimeric	0	1	564477	3	50M	*	0	0	AGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCT	BAABCFFFFFFFGGGGGGGGFGHGFHGGGGGGGGGGGHHHHGGGGHHHHF	XC:Z:GACATGATAGAC	MD:Z:50	XF:Z:INTERGENIC	PG:Z:STAR	RG:Z:00000.1	XG:Z:RP5-857K21.4	NH:i:2	NM:i:0	XM:Z:-	UQ:i:0	AS:i:49	gf:Z:INTRONIC	gn:Z:RP5-857K21.4	gs:Z:-