[med-svn] [Git][med-team/drop-seq][master] 4 commits: New upstream version 2.5.3+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / drop-seq


Commits:
f0cb7659 by Pierre Gruet at 2023-06-25T14:43:52+02:00
New upstream version 2.5.3+dfsg
- - - - -
9637b53d by Pierre Gruet at 2023-06-25T14:45:17+02:00
Update upstream source from tag 'upstream/2.5.3+dfsg'

Update to upstream version '2.5.3+dfsg'
with Debian dir 9667b6075506ad7994b70b2442371eeaeb1cfc84
- - - - -
1ad4b2ad by Pierre Gruet at 2023-06-25T14:46:18+02:00
Updating changelog

- - - - -
8887ed0e by Pierre Gruet at 2023-06-25T14:46:36+02:00
Upload to unstable

- - - - -


24 changed files:

- build.xml
- debian/changelog
- src/ant/defs.xml
- + src/java/org/broadinstitute/dropseqrna/barnyard/ChimericUmi.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/ChimericUmiCollection.java
- + src/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReads.java
- + src/tests/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReadsTest.java
- + testdata/org/broadinstitute/dropseq/barnyard/6T.chimeric_read_metrics
- + testdata/org/broadinstitute/dropseq/barnyard/6T.chimeric_report.txt
- + testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.6T.sam
- + testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.both.sam
- + testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.input.sam
- + testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.input2.sam
- + testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.umiReuse.sam
- + testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.umiReuse10x.sam
- + testdata/org/broadinstitute/dropseq/barnyard/both.chimeric_read_metrics
- + testdata/org/broadinstitute/dropseq/barnyard/both.chimeric_report.txt
- + testdata/org/broadinstitute/dropseq/barnyard/ed_collapse.chimeric_report.txt
- + testdata/org/broadinstitute/dropseq/barnyard/selectedCellBarcodes.txt
- + testdata/org/broadinstitute/dropseq/barnyard/two_cells.chimeric_report.txt
- + testdata/org/broadinstitute/dropseq/barnyard/umiReuse.chimeric_read_metrics
- + testdata/org/broadinstitute/dropseq/barnyard/umiReuse.chimeric_report.txt
- + testdata/org/broadinstitute/dropseq/barnyard/umiReuse10x.chimeric_read_metrics
- + testdata/org/broadinstitute/dropseq/barnyard/umiReuse10x.chimeric_report.txt


Changes:

=====================================
build.xml
=====================================
@@ -139,6 +139,7 @@
         <package-command visibility="public" title="BaseDistributionAtReadPosition"/>
         <package-command visibility="public" title="TagReadWithInterval"/>
         <package-command visibility="public" title="DigitalExpression"/>
+    	<package-command visibility="public" title="MarkChimericReads"/>
         <package-command visibility="public" title="GatherMolecularBarcodeDistributionByGene"/>
         <package-command visibility="public" title="SingleCellRnaSeqMetricsCollector"/>
         <package-command visibility="public" title="PolyATrimmer"/>


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+drop-seq (2.5.3+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.5.3+dfsg
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 25 Jun 2023 14:46:21 +0200
+
 drop-seq (2.5.2+dfsg-1) unstable; urgency=medium
 
   * New upstream version 2.5.2+dfsg


=====================================
src/ant/defs.xml
=====================================
@@ -32,7 +32,7 @@
 <property name="repository.revision" value=""/>
 
 
-<property name="Drop-seq.version" value="2.5.2"/>
+<property name="Drop-seq.version" value="2.5.3"/>
 <property name="zip.label" value="Drop-seq_tools-${Drop-seq.version}"/>
 <property name="javac.debug" value="true"/>
 <property name="javac.target" value="1.8"/>


=====================================
src/java/org/broadinstitute/dropseqrna/barnyard/ChimericUmi.java
=====================================
@@ -0,0 +1,87 @@
+package org.broadinstitute.dropseqrna.barnyard;
+
+import java.util.Collections;
+import java.util.Set;
+
+import org.broadinstitute.dropseqrna.utils.ObjectCounter;
+
+public class ChimericUmi {
+	
+	private final String molecularBarcode;	
+	private final Set<String> chimericGenes;
+	
+	public enum CHIMERIC_STRATEGY {
+    	REMOVE_ALL, RETAIN_MOST_SUPPORTED;
+    }
+
+	/**
+	 * Construct a ChimericUmi object for a single cell.
+	 * This object receives the number of reads supporting each gene for a cell and UMI sequence, and based on the strategy
+	 * remembers the set of genes that are chimeric.
+	 * @param molecularBarcode The molecular barcode
+	 * @param genes A collection of gene symbols with the number of supporting reads for this cell/molecular barcode.
+	 * @param strategy The strategy to discover chimeric reads.  REMOVE_ALL removes all genes for this UMI if there is more than 1 gene.  RETAIN_MOST_SUPPORTED retains
+	 * the gene with the highest read count and flags all other genes as chimeric.  If the most supported gene is ambiguous (there are multiple genes with the highest count) then 
+	 * all genes are chimeric. 
+	 */
+	public ChimericUmi(String molecularBarcode, ObjectCounter<String> genes, CHIMERIC_STRATEGY strategy) {
+		this.molecularBarcode=molecularBarcode;
+		this.chimericGenes=getChimericGenes(genes,strategy);
+	}
+
+	public String getMolecularBarcode() {
+		return molecularBarcode;
+	}
+	
+	public Set<String> getChimericGenes() {
+		return chimericGenes;
+	}
+	
+	/**
+	 * Find the set of 0 or more genes where the UMI 
+	 * @return
+	 */
+	static Set<String> getChimericGenes (ObjectCounter<String> genes, CHIMERIC_STRATEGY strategy) {    		
+		switch (strategy) {
+		case REMOVE_ALL: return (getChimericGenesRemoveAll(genes));
+		case RETAIN_MOST_SUPPORTED: return(getChimericGenesRetainMostSupported(genes));
+		default: 
+			throw new IllegalArgumentException("Chimeric Strategy not supported");
+		}			
+	}
+	
+	/**
+	 * Simple strategy to filter chimeric genes.  If multiple genes share the same UMI, all genes are chimeric.
+	 * @param genes
+	 * @return
+	 */
+	static Set <String> getChimericGenesRemoveAll(ObjectCounter<String> genes) {
+		if (genes.getSize()<2) return Collections.emptySet();
+		return (Set<String>) genes.getKeys();
+	}
+	
+	/**
+	 * If there are multiple genes with varying degrees of support, flag all but the most
+	 * supported gene as chimeric.  If multiple genes are the most supported, the result is ambiguous
+	 * and all genes for this UMI are considered chimeric.
+	 * @param genes A set of genes with read counts
+	 * @return A set of chimeric gene symbols.  This set can be empty.
+	 */
+	static Set<String> getChimericGenesRetainMostSupported(ObjectCounter<String> genes) {
+		// no chimeric genes.
+		if (genes.getSize()<2) return Collections.emptySet();
+		// at least one chimeric gene.
+		String mostSupportedGene=genes.getMax();
+		int counts = genes.getCountForKey(mostSupportedGene);
+		int genesAtSupport=genes.getNumberOfSize(counts);
+		if (genesAtSupport==1) {
+			Set<String> chimeric = (Set<String>) genes.getKeys();
+			chimeric.remove(mostSupportedGene);
+			return chimeric;
+		}			
+		// ambiguous, return all genes as chimeric.
+		return (Set<String>)genes.getKeys();		
+	}
+
+	
+}
\ No newline at end of file


=====================================
src/java/org/broadinstitute/dropseqrna/barnyard/ChimericUmiCollection.java
=====================================
@@ -0,0 +1,164 @@
+package org.broadinstitute.dropseqrna.barnyard;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.broadinstitute.dropseqrna.barnyard.ChimericUmi.CHIMERIC_STRATEGY;
+import org.broadinstitute.dropseqrna.barnyard.digitalexpression.UMICollection;
+import org.broadinstitute.dropseqrna.utils.ObjectCounter;
+
+import htsjdk.samtools.util.Log;
+
+/**
+ * A collection of all chimeric UMIs / genes for a single cell.
+ * @author nemesh
+ *
+ */
+public class ChimericUmiCollection {
+
+	private static final Log log = Log.getInstance(ChimericUmiCollection.class);
+	
+	private final String cellBarcode;
+	// map from a UMI to the genes that are chimeric for that UMI.
+	private Map<String, ChimericUmi> map;
+	// key is the molecular barcode, value is the number of reads per gene.
+	
+	private Set<String> problematicUmis;
+
+	private Map<String, ObjectCounter<String>> umiGeneSupport;
+	private boolean isFinal = false;
+	private final ChimericUmi.CHIMERIC_STRATEGY strategy;
+	private int totalUMIs=0;
+	
+	
+	public ChimericUmiCollection (String cellBarcode, ChimericUmi.CHIMERIC_STRATEGY strategy) {
+		this.cellBarcode=cellBarcode;
+		this.strategy=strategy;
+		totalUMIs=0;
+		map = new HashMap<>();
+		// A map from the UMI sequence to the genes that belong to that UMI with the number of reads per gene.
+		// This will be removed when the data is finalized to save memory.
+		umiGeneSupport = new HashMap<String, ObjectCounter<String>>();
+		this.problematicUmis=new HashSet<>();
+	}
+		
+	/**
+	 * Add data from a UMICollection directly.
+	 * @param u
+	 */
+	public void add (UMICollection u) {
+		add(u.getGeneName(), u.getMolecularBarcodeCounts());
+	}
+	
+	/**
+	 * Add data for a single gene and the collection of molecular barcodes for that gene with their corresponding read counts
+	 * @param gene
+	 * @param molBCCounts
+	 */
+	public void add (String gene, ObjectCounter<String> molBCCounts) {
+		if (isFinal) 
+			throw new IllegalStateException("This object has been finalized, no more data can be added");
+		
+		for (String molBC: molBCCounts.getKeys()) {
+			
+    		int support = molBCCounts.getCountForKey(molBC);
+    		ObjectCounter<String> geneSupportCounts = umiGeneSupport.get(molBC);
+    		if (geneSupportCounts==null) {
+    			geneSupportCounts=new ObjectCounter<>();
+    			umiGeneSupport.put(molBC, geneSupportCounts);
+    		}
+    		geneSupportCounts.incrementByCount(gene, support);
+    		totalUMIs = getTotalUMIs() + 1;
+    	}
+	}
+		
+	/**
+	 * Get a list of 0 or more genes that are chimeric for the requested UMI.
+	 * When this method is called the object is finalized and no more data can be added. 
+	 * @param umi A molecular barcode to query
+	 * @return A set with 0 or more entries of chimeric genes.  If the UMI does not exist for this cell, return an empty set of genes.
+	 */
+	public Set<String> getChimericGenes (String umi) {		
+		if (isFinal==false) 
+			buildChimericUmis();
+		ChimericUmi cu = map.get(umi);
+		if (cu==null)
+			return Collections.emptySet();
+		return cu.getChimericGenes();
+	}
+	
+	/**
+	 * Checks if a UMI is chimeric, either via the chimerism test or via additionally registered UMIs that are problematic.
+	 * @param umi The molecular barcode to test.
+	 * @return true if the read is chimeric, or has been registered as problematic.
+	 */
+	public boolean isChimericOrProblematic (String umi, String gene) {
+		if (isFinal==false) 
+			buildChimericUmis();
+		if (this.problematicUmis.contains(umi))
+			return true;
+		Set<String> chimericGenes = getChimericGenes(umi);
+		return chimericGenes.contains(gene);		
+	}
+	
+	/**
+	 * Record that a UMI is problematic for this cell by a different test than the chimeric read test.
+	 * @param umi
+	 */
+	public void registerProblematicUmi (String umi) {
+		this.problematicUmis.add(umi);
+	}
+	
+	public Set<String> getChimericUmis () {
+		return map.keySet();
+	}
+	
+	public Set<String> getProblematicUmis() {
+		return problematicUmis;
+	}
+
+		
+	
+	/**
+	 * Finalize the data set.  Chimeric UMIs are discovered from the input data.
+	 * Input data is discarded to save memory, and no more data can be added.
+	 * It is recommended to finalize each cell barcode's data as it is entered to save memory 
+	 * since only the genes that are chimeric for a given molecular barcode are retained.
+	 */	
+	public void buildChimericUmis () {		
+		for (String molBC: umiGeneSupport.keySet()) {
+			ChimericUmi cu = new ChimericUmi(molBC, umiGeneSupport.get(molBC), this.strategy);
+			map.put(molBC, cu);
+		}
+		this.isFinal=true;
+		this.umiGeneSupport=null;
+	}
+
+	public String getCellBarcode() {
+		return cellBarcode;
+	}
+
+	public int getTotalUMIs() {		
+		return totalUMIs;
+	}
+	
+	/**
+	 * Find the number of chimeric UMI/gene pairs for this cell.
+	 * @return
+	 */
+	public int getTotalUMisChimeric() {
+		if (isFinal==false) 
+			buildChimericUmis();
+		int count=0;
+		for (String umi: this.map.keySet()) {
+			count+=map.get(umi).getChimericGenes().size();
+		}
+		return (count);
+	}
+	
+	
+	
+}


=====================================
src/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReads.java
=====================================
@@ -0,0 +1,347 @@
+/*
+ * MIT License
+ *
+ * Copyright 2021 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.barnyard;
+
+import com.google.common.base.CharMatcher;
+import htsjdk.samtools.SAMFileWriter;
+import htsjdk.samtools.SAMFileWriterFactory;
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.metrics.MetricBase;
+import htsjdk.samtools.metrics.MetricsFile;
+import htsjdk.samtools.util.*;
+import org.apache.commons.lang.StringUtils;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.dropseqrna.barnyard.ChimericUmi.CHIMERIC_STRATEGY;
+import org.broadinstitute.dropseqrna.barnyard.digitalexpression.UMICollection;
+import org.broadinstitute.dropseqrna.cmdline.CustomCommandLineValidationHelper;
+import org.broadinstitute.dropseqrna.cmdline.DropSeq;
+import org.broadinstitute.dropseqrna.utils.FileListParsingUtils;
+import org.broadinstitute.dropseqrna.utils.ObjectCounter;
+import org.broadinstitute.dropseqrna.utils.OutputWriterUtil;
+import org.broadinstitute.dropseqrna.utils.SamHeaderUtil;
+import org.broadinstitute.dropseqrna.utils.StringInterner;
+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;
+import java.io.IOException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+ at CommandLineProgramProperties(summary = "Identify UMIs assigned to multiple genes in the same cell, then mark reads for such cell and UMI "
+		+ "by adjusting the MAPQ, and/or generate a report for genes and UMIs in selected cells.", oneLineSummary = "Mark reads with UMIs that are assigned to multiple genes.", programGroup = DropSeq.class)
+public class MarkChimericReads extends GeneFunctionCommandLineBase {
+	private static final Log log = Log.getInstance(MarkChimericReads.class);
+	
+	private static final CHIMERIC_STRATEGY DEFAULT_STRATEGY = CHIMERIC_STRATEGY.RETAIN_MOST_SUPPORTED;
+	public static final String CHIMERIC_COLUMN = "CHIMERIC";
+
+	@Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM or BAM file to analyze. This argument can accept wildcards, or a file with the "
+			+ "suffix .bam_list that contains the locations of multiple BAM files", minElements = 1)
+	public List<File> INPUT;
+
+	@Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "SAM or BAM file with MAPQ of putative "
+			+ "chimeric reads adjusted.", optional = true)
+	public File OUTPUT;
+	
+	@Argument(doc="The strategy to use to detect and filter chimeric reads.  REMOVE_ALL marks all genes that share the same UMI on the same cell.  "
+			+ "RETAIN_MOST_SUPPORTED retains the gene with the largest number of reads for a UMI/cell.  If RETAIN_MOST_SUPPORTED most suported gene is ambiguous,"
+			+ "then all genes/UMI pairs are flagged as chimeric.", optional=false)
+	public ChimericUmi.CHIMERIC_STRATEGY STRATEGY=DEFAULT_STRATEGY;
+
+	@Argument(doc = "List of CELL_BARCODES to evaluate for chimeric reads.", optional=true)
+	public File CELL_BC_FILE;
+
+	@Argument(doc = "Tab-separated file with a row for each {CELL_BARCODE, MOLECULAR_BARCODE} found in selected cells, "
+			+ "with the number of observations and chimeric status.  This file can end with .gz to be gzipped, which is recommended for larger data sets.", optional = true)
+	public File OUTPUT_REPORT;
+
+	@Argument(doc = "Produce report of number of unique {CELL_BARCODE, MOLECULAR_BARCODE}, and number marked.", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME, optional = true)
+	public File METRICS;
+
+	@Argument(doc = "Mark as chimeric all reads in which the {CELL_BARCODE, MOLECULAR_BARCODE} is assigned to multiple genes.")
+	public boolean MARK_UMI_REUSE = true;
+
+	@Argument(doc = "Mark as chimeric reads with UMIs containing at least this many Ts.", optional = true)
+	public Integer T_RICH_THRESHOLD;
+
+	@Argument(doc = "Ignore reads with MAPQ < this when making chimeric determination.")
+	public Integer READ_MQ = 10;
+
+	@Argument(doc = "Tag in which to store original MAPQ, if read is marked as chimeric.  " + "Set to NULL to suppress tag creation.", optional = true)
+	public String MAPQ_TAG = "YM";
+
+	@Argument(doc = "Chimeric reads are tagged by setting MAPQ to this value.")
+	public int CHIMERIC_MAPQ = 0;
+
+	@Argument(doc = "The cell barcode tag.")
+	public String CELL_BARCODE_TAG = "XC";
+
+	@Argument(doc = "The molecular barcode tag.")
+	public String MOLECULAR_BARCODE_TAG = "XM";
+
+	@Override
+	protected String[] customCommandLineValidation() {
+		if (OUTPUT != null) {
+			IOUtil.assertFileIsWritable(OUTPUT);
+		}
+		if (OUTPUT_REPORT != null) {
+			IOUtil.assertFileIsWritable(OUTPUT_REPORT);
+		}
+
+		final ArrayList<String> list = new ArrayList<>(1);
+		if (OUTPUT == null && OUTPUT_REPORT == null) {
+			list.add("It does not make sense for neither OUTPUT nor OUTPUT_REPORT to be set.");
+		}
+		return CustomCommandLineValidationHelper.makeValue(super.customCommandLineValidation(), list);
+	}
+
+	@Override
+	protected int doWork() {
+		INPUT = FileListParsingUtils.expandFileList(INPUT);
+
+		// FIRST PASS: accumulate chimeric UMIs for each CBC, and optionally write report
+		final Map<String, ChimericUmiCollection> chimerics = identifyChimericsAndWriteReport(MARK_UMI_REUSE, T_RICH_THRESHOLD);
+
+		// PASS 2: Write BAM with chimeric reads marked.
+		if (OUTPUT != null) {
+			long numMarked = markReads(chimerics);
+			log.info(numMarked + " reads marked chimeric.");
+		}
+
+		return 0;
+	}
+
+	private long markReads(final Map<String, ChimericUmiCollection> chimerics) {
+		final GeneFunctionProcessor p = new GeneFunctionProcessor(GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG, false, STRAND_STRATEGY, LOCUS_FUNCTION_LIST);		
+		
+		long numMarked = 0;
+		SamHeaderAndIterator headerAndIter = SamFileMergeUtil.mergeInputs(this.INPUT, false, SamReaderFactory.makeDefault());
+		SamHeaderUtil.addPgRecord(headerAndIter.header, this);
+		SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(headerAndIter.header, true, OUTPUT);
+		ProgressLogger progLog = new ProgressLogger(log, 1000000, "marked");
+		log.info("Marking chimeric UMIs in BAM");
+		for (final SAMRecord rec : new IterableAdapter<>(headerAndIter.iterator)) {
+			progLog.record(rec);
+			// Parse the gene function tags, and get the interpreted tags for the given filters.
+			// Using a deep copy of the record because otherwise processRead alters the record as a side effect.
+			// TODO: should processRead  be making a deep copy internally to avoid the side effect?
+			List<SAMRecord> processedRec =  p.processRead (rec.deepCopy());
+			
+			// only process the record for chimeric tags if the read can be interpreted with one consistent gene.
+			if (processedRec.size()==1) {
+				String geneName = processedRec.get(0) .getStringAttribute(GENE_NAME_TAG);
+				String umi = rec.getStringAttribute(MOLECULAR_BARCODE_TAG);
+				ChimericUmiCollection cuc = chimerics.get(rec.getStringAttribute(CELL_BARCODE_TAG));	
+				if (cuc!=null && cuc.isChimericOrProblematic(umi, geneName)) {
+					markChimeric(rec);
+					++numMarked;
+				}
+			}						
+			out.addAlignment(rec);
+		}
+		out.close();
+		CloserUtil.close(headerAndIter.iterator);
+		return numMarked;
+	}
+
+	private void markChimeric(final SAMRecord rec) {
+		if (MAPQ_TAG != null) {
+			rec.setAttribute(MAPQ_TAG, rec.getMappingQuality());
+		}
+		rec.setMappingQuality(CHIMERIC_MAPQ);
+	}
+
+	private static void writePerTranscriptHeader(final BufferedWriter out) {
+		String[] header = { GatherMolecularBarcodeDistributionByGene.COLUMN_LABEL.CELL_BARCODE.toString(),
+				GatherMolecularBarcodeDistributionByGene.COLUMN_LABEL.GENE.toString(),
+				GatherMolecularBarcodeDistributionByGene.COLUMN_LABEL.MOLECULAR_BARCODE.toString(),
+				GatherMolecularBarcodeDistributionByGene.COLUMN_LABEL.NUM_OBS.toString(), CHIMERIC_COLUMN};
+		String h = StringUtils.join(header, "\t");
+		OutputWriterUtil.writeResult(h, out);
+	}
+	
+	private void writePerTranscriptStats(final String gene, final String cellBarcode, final ObjectCounter<String> counts, final ChimericUmiCollection chimerics,
+			final BufferedWriter out, final MarkChimericReadMetrics metrics) {
+				
+		for (String key : counts.getKeys()) {
+			int value = counts.getCountForKey(key);
+			boolean chimeric = chimerics.isChimericOrProblematic(key, gene);
+			String[] line = { cellBarcode, gene, key, Integer.toString(value), Boolean.toString(chimeric) };
+			if (chimeric) {
+				++metrics.NUM_MARKED_UMIS;
+			}
+			String h = StringUtils.join(line, "\t");
+			OutputWriterUtil.writeResult(h, out);
+		}
+	}
+	
+	
+	/**
+     * @return Map with key=CBC, value=Set of chimeric UMIs for that CBC
+     */
+    private Map<String, ChimericUmiCollection> identifyChimericsAndWriteReport(boolean markUmiReuse, Integer tRichThreshold) {
+        final BufferedWriter report_out;
+        if (OUTPUT_REPORT != null) {
+            IOUtil.assertFileIsWritable(OUTPUT_REPORT);
+            report_out = IOUtil.openFileForBufferedWriting(OUTPUT_REPORT);
+
+            writePerTranscriptHeader(report_out);
+        } else {
+            report_out = null;
+        }
+        
+        // Set up the cell barcodes.  Can be null to try and repair the whole BAM.
+        final Set<String> cellBarcodes=getCellBarcodes();       
+        
+        PeekableIterator<UMICollection> umiIterator = new PeekableIterator<>(
+                new UMIIterator(SamFileMergeUtil.mergeInputs(this.INPUT, false),
+                        GENE_NAME_TAG, GENE_STRAND_TAG, GENE_FUNCTION_TAG,
+                        this.STRAND_STRATEGY, this.LOCUS_FUNCTION_LIST, this.CELL_BARCODE_TAG, this.MOLECULAR_BARCODE_TAG,
+                        this.READ_MQ, false, cellBarcodes, true, false));
+
+        // Remember {CBC, UMI, Gene} pairs to be marked chimeric
+        final Map<String, ChimericUmiCollection> chimerics = new HashMap<>();
+        final MarkChimericReadMetrics metrics = new MarkChimericReadMetrics();
+
+        // TODO: Is this premature optimization?  Genes will be reused across many cells so should be useful.
+        StringInterner  geneStringCache = new StringInterner();
+        
+        // progress logger
+        ProgressLogger progLog = new ProgressLogger(log, 100, "cells chimeric marked");
+        
+        while (umiIterator.hasNext()) {
+        	
+            final String cellBarcode = umiIterator.peek().getCellBarcode();
+            progLog.record(cellBarcode, 0);
+            ChimericUmiCollection cuc = new ChimericUmiCollection(cellBarcode, this.STRATEGY);
+            
+            final List<UMICollection> umiCollectionsForCell = new ArrayList<>();
+            
+            // retain Alec's comments about slurping up data.
+            while (umiIterator.hasNext() && cellBarcode.equals(umiIterator.peek().getCellBarcode())) {
+            	UMICollection umiC= umiIterator.next();
+            	// only add items if you want to find chimeras later.  If polyA only then this is false.
+            	if (markUmiReuse) 
+            		cuc.add(geneStringCache.intern(umiC.getGeneName()), umiC.getMolecularBarcodeCounts());
+            		// cuc.add(umiC);
+            	umiCollectionsForCell.add(umiC);
+            }
+            // finalize the collection.
+            cuc.buildChimericUmis();
+                        
+            if (markUmiReuse) {                
+                // Count number of UMIs for this CBC in case emitting metrics file.
+                metrics.NUM_UMIS += cuc.getTotalUMIs();
+                metrics.NUM_REUSED_UMIS += cuc.getTotalUMisChimeric();
+            }
+            
+            if (tRichThreshold != null) {
+                final Set<String> umisForCellBarcode = new HashSet<>();
+                umiCollectionsForCell.forEach(umiCollection -> umisForCellBarcode.addAll(umiCollection.getMolecularBarcodeCounts().getKeys()));
+                if (!markUmiReuse && METRICS != null) {
+                    // Count number of UMIs for this CBC in case emitting metrics file, and not counted above
+                    metrics.NUM_UMIS += umiCollectionsForCell.stream().mapToLong(umiCollection -> umiCollection.getMolecularBarcodeCounts().getSize()).sum();
+                }
+                final CharMatcher tMatcher = CharMatcher.is('T');
+                final Collection<String> polyTUmis = umisForCellBarcode.stream().filter(umi -> tMatcher.countIn(umi) >= tRichThreshold).collect(Collectors.toList());
+                metrics.NUM_T_RICH_UMIS += polyTUmis.size();
+                polyTUmis.forEach(cuc::registerProblematicUmi);
+            }
+                        
+            chimerics.put(cellBarcode, cuc);
+            if (report_out != null) {
+                for (final UMICollection batch : umiCollectionsForCell) {
+                	
+                    writePerTranscriptStats(batch.getGeneName(), batch.getCellBarcode(),
+                            batch.getMolecularBarcodeCounts(), cuc, report_out, metrics);
+                }
+            }
+        }
+        CloserUtil.close(umiIterator);
+        
+        log.info("Total cell/UMIs observed [" +metrics.NUM_UMIS+"] Marked Chimeric [" + metrics.NUM_MARKED_UMIS+"] % ["+ String.format("%.2f%%",metrics.getPercentMarked())+"]");
+        
+        try {
+            if (report_out != null) {
+                report_out.close();
+            }
+        } catch (IOException e) {
+            throw new RuntimeIOException("Exception writing " + OUTPUT_REPORT, e);
+        }
+
+        if (METRICS != null) {
+            final MetricsFile<MarkChimericReadMetrics, Integer> metricsFile = new MetricsFile<>();
+            metricsFile.addMetric(metrics);
+            metricsFile.write(METRICS);
+        }
+
+        return chimerics;
+    }
+    
+    private Set<String> getCellBarcodes () {
+		if (CELL_BC_FILE==null)  {
+			log.info("No cell barcode file - will process all cell barcodes");
+			return null;
+        }        	        
+         	
+		Set<String> cellBarcodes=new HashSet<>(ParseBarcodeFile.readCellBarcodeFile(CELL_BC_FILE));
+    	log.info("Found " + cellBarcodes.size()+ " cell barcodes in file");
+    	return cellBarcodes;
+	}
+	
+	public static class MarkChimericReadMetrics extends MetricBase {
+		public long NUM_UMIS;
+		public long NUM_MARKED_UMIS;
+		public long NUM_T_RICH_UMIS;
+		public long NUM_REUSED_UMIS;
+		
+		public double getPercentMarked () {
+			return ((double) NUM_MARKED_UMIS / (double) NUM_UMIS)*100;
+		}
+
+		/**
+		 * Adds the non-calculated metrics (which is all of them)
+		 */
+		public void merge(final MarkChimericReadMetrics metric) {
+			this.NUM_UMIS += metric.NUM_UMIS;
+			this.NUM_MARKED_UMIS += metric.NUM_MARKED_UMIS;
+			this.NUM_T_RICH_UMIS += metric.NUM_T_RICH_UMIS;
+			this.NUM_REUSED_UMIS += metric.NUM_REUSED_UMIS;
+		}
+	}
+
+	/** Stock main method. */
+	public static void main(final String[] args) {
+		new MarkChimericReads().instanceMainWithExit(args);
+	}
+}


=====================================
src/tests/java/org/broadinstitute/dropseqrna/barnyard/MarkChimericReadsTest.java
=====================================
@@ -0,0 +1,116 @@
+/*
+ * MIT License
+ *
+ * Copyright 2021 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.barnyard;
+
+import org.broadinstitute.dropseqrna.barnyard.MarkChimericReads;
+import org.broadinstitute.dropseqrna.barnyard.ChimericUmi.CHIMERIC_STRATEGY;
+import org.broadinstitute.dropseqrna.utils.TestUtils;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.Arrays;
+
+public class MarkChimericReadsTest {
+	public static File TEST_DATA_DIR = new File("testdata/org/broadinstitute/dropseq/barnyard");
+	public static final File CELL_BC_FILE = new File(TEST_DATA_DIR, "selectedCellBarcodes.txt");
+	public static final File EXPECTED_CHIMERIC_REPORT = new File(TEST_DATA_DIR, "umiReuse.chimeric_report.txt");
+
+	@Test(enabled = true)
+	public void testUmiReuse() {
+		final MarkChimericReads clp = new MarkChimericReads();
+		clp.OUTPUT = TestUtils.getTempReportFile("MarkChimericReads.", ".sam");
+		clp.OUTPUT.deleteOnExit();
+		clp.OUTPUT_REPORT = TestUtils.getTempReportFile("chimeric_report.", ".txt");
+		clp.OUTPUT_REPORT.deleteOnExit();
+		clp.METRICS = TestUtils.getTempReportFile("MarkChimericReads.", ".chimeric_read_metrics");
+		clp.METRICS.deleteOnExit();
+		clp.INPUT = Arrays.asList(new File(TEST_DATA_DIR, "MarkChimericReads.input.sam"));
+		clp.CELL_BC_FILE = CELL_BC_FILE;
+		Assert.assertEquals(clp.doWork(), 0);
+		TestUtils.assertSamFilesSame(clp.OUTPUT, new File(TEST_DATA_DIR, "MarkChimericReads.umiReuse.sam"), false);
+		Assert.assertTrue(TestUtils.testFilesSame(clp.OUTPUT_REPORT, EXPECTED_CHIMERIC_REPORT));
+		Assert.assertTrue(TestUtils.testFilesSame(clp.METRICS, new File(TEST_DATA_DIR, "umiReuse.chimeric_read_metrics")));
+	}
+
+	// MarkChimericReads.input2.sam
+	@Test(enabled = true)
+	public void testUmiReuse10xStrategy() {
+		// in this case, for molecular barcode ATTTAGTAAATG, there are 2 reads for USMG5 but only one for CXorf56.
+		// USMG5 is retained, CXorf56 is marked as chimeric.
+		// This is the 10x strategy for removing chimeric reads
+		final MarkChimericReads clp = new MarkChimericReads();
+		clp.OUTPUT = TestUtils.getTempReportFile("MarkChimericReads.", ".sam");
+		clp.OUTPUT.deleteOnExit();
+		clp.OUTPUT_REPORT = TestUtils.getTempReportFile("chimeric_report.", ".txt");
+		clp.OUTPUT_REPORT.deleteOnExit();
+		clp.METRICS = TestUtils.getTempReportFile("MarkChimericReads.", ".chimeric_read_metrics");
+		clp.METRICS.deleteOnExit();
+		clp.INPUT = Arrays.asList(new File(TEST_DATA_DIR, "MarkChimericReads.input2.sam"));
+		clp.CELL_BC_FILE = new File(TEST_DATA_DIR, "selectedCellBarcodes.txt");
+		clp.STRATEGY = CHIMERIC_STRATEGY.RETAIN_MOST_SUPPORTED;
+		Assert.assertEquals(clp.doWork(), 0);
+		TestUtils.assertSamFilesSame(clp.OUTPUT, new File(TEST_DATA_DIR, "MarkChimericReads.umiReuse10x.sam"), false);
+		Assert.assertTrue(TestUtils.testFilesSame(clp.OUTPUT_REPORT, new File(TEST_DATA_DIR, "umiReuse10x.chimeric_report.txt")));
+		Assert.assertTrue(TestUtils.testFilesSame(clp.METRICS, new File(TEST_DATA_DIR, "umiReuse10x.chimeric_read_metrics")));
+	}
+
+	@Test(enabled = true)
+	public void testPolyT() {
+		final MarkChimericReads clp = new MarkChimericReads();
+		clp.OUTPUT = TestUtils.getTempReportFile("MarkChimericReads.", ".sam");
+		clp.OUTPUT.deleteOnExit();
+		clp.OUTPUT_REPORT = TestUtils.getTempReportFile("chimeric_report.", ".txt");
+		clp.OUTPUT_REPORT.deleteOnExit();
+		clp.METRICS = TestUtils.getTempReportFile("MarkChimericReads.", ".chimeric_read_metrics");
+		clp.METRICS.deleteOnExit();
+		clp.INPUT = Arrays.asList(new File(TEST_DATA_DIR, "MarkChimericReads.input.sam"));
+		clp.CELL_BC_FILE = new File(TEST_DATA_DIR, "selectedCellBarcodes.txt");
+		clp.MARK_UMI_REUSE = false;
+		clp.T_RICH_THRESHOLD = 6;
+		Assert.assertEquals(clp.doWork(), 0);
+		TestUtils.assertSamFilesSame(clp.OUTPUT, new File(TEST_DATA_DIR, "MarkChimericReads.6T.sam"), false);
+		Assert.assertTrue(TestUtils.testFilesSame(clp.OUTPUT_REPORT, new File(TEST_DATA_DIR, "6T.chimeric_report.txt")));
+		Assert.assertTrue(TestUtils.testFilesSame(clp.METRICS, new File(TEST_DATA_DIR, "6T.chimeric_read_metrics")));
+	}
+
+	@Test(enabled = true)
+	public void testBoth() {
+		final MarkChimericReads clp = new MarkChimericReads();
+		clp.OUTPUT = TestUtils.getTempReportFile("MarkChimericReads.", ".sam");
+		clp.OUTPUT.deleteOnExit();
+		clp.OUTPUT_REPORT = TestUtils.getTempReportFile("chimeric_report.", ".txt");
+		clp.OUTPUT_REPORT.deleteOnExit();
+		clp.METRICS = TestUtils.getTempReportFile("MarkChimericReads.", ".chimeric_read_metrics");
+		clp.METRICS.deleteOnExit();
+		clp.INPUT = Arrays.asList(new File(TEST_DATA_DIR, "MarkChimericReads.input.sam"));
+		clp.CELL_BC_FILE = new File(TEST_DATA_DIR, "selectedCellBarcodes.txt");
+		clp.T_RICH_THRESHOLD = 6;
+		Assert.assertEquals(clp.doWork(), 0);
+		TestUtils.assertSamFilesSame(clp.OUTPUT, new File(TEST_DATA_DIR, "MarkChimericReads.both.sam"), false);
+		Assert.assertTrue(TestUtils.testFilesSame(clp.OUTPUT_REPORT, new File(TEST_DATA_DIR, "both.chimeric_report.txt")));
+		Assert.assertTrue(TestUtils.testFilesSame(clp.METRICS, new File(TEST_DATA_DIR, "both.chimeric_read_metrics")));
+	}
+
+}


=====================================
testdata/org/broadinstitute/dropseq/barnyard/6T.chimeric_read_metrics
=====================================
@@ -0,0 +1,6 @@
+
+## METRICS CLASS	org.broadinstitute.dropseqrna.priv.barnyard.MarkChimericReads$MarkChimericReadMetrics
+NUM_UMIS	NUM_MARKED_UMIS	NUM_T_RICH_UMIS	NUM_REUSED_UMIS
+163	20	20	0
+
+


=====================================
testdata/org/broadinstitute/dropseq/barnyard/6T.chimeric_report.txt
=====================================
@@ -0,0 +1,165 @@
+CELL_BARCODE	GENE	MOLECULAR_BARCODE	NUM_OBS	CHIMERIC
+ACCAAACGTTCTCACC	AC025594.3	TACATTACAGCT	1	false
+ACCAAACGTTCTCACC	ACOT13	AGAGTAATATGA	1	false
+ACCAAACGTTCTCACC	AFF4	TAAACTGTTTAA	1	false
+ACCAAACGTTCTCACC	AJAP1	CCGGATTATTGC	1	false
+ACCAAACGTTCTCACC	AL645728.1	CTGCGATTACGG	1	false
+ACCAAACGTTCTCACC	ALDOA	CTTCTGCAATGG	1	false
+ACCAAACGTTCTCACC	ALG1L9P	CCAGCGCTAATT	1	false
+ACCAAACGTTCTCACC	ANKRD10	AATTTTATGAAT	1	true
+ACCAAACGTTCTCACC	ANKRD10-IT1	ATCCTCGTTCTG	1	false
+ACCAAACGTTCTCACC	AP3B2	ACTCGGATACCT	1	false
+ACCAAACGTTCTCACC	APBA2	CATCCTGCGGGC	1	false
+ACCAAACGTTCTCACC	ARGLU1	ACGAGTATTGCC	1	false
+ACCAAACGTTCTCACC	ARHGEF3	TATTTGTCTGAG	1	true
+ACCAAACGTTCTCACC	ARNT2	TGCTATCTTAAC	1	false
+ACCAAACGTTCTCACC	ARPP21	CTGTGTTAATTG	1	true
+ACCAAACGTTCTCACC	ATAD1	AGAAGACGGCCG	1	false
+ACCAAACGTTCTCACC	ATP9B	AGCAAGCACCGA	1	false
+ACCAAACGTTCTCACC	BRD1	GCACTCATTTCG	1	false
+ACCAAACGTTCTCACC	C19orf66	AAAATTTGGCAA	1	false
+ACCAAACGTTCTCACC	CACNA1A	TCACCTCCATAC	1	false
+ACCAAACGTTCTCACC	CAMK1D	ATGATGGTAACA	1	false
+ACCAAACGTTCTCACC	CAPZB	GCATGCTTAGAT	1	false
+ACCAAACGTTCTCACC	CBL	TAACCCTATGAT	1	false
+ACCAAACGTTCTCACC	CCDC3	GACATGGCTCAC	1	false
+ACCAAACGTTCTCACC	CCDC84	TCTCTAGGGTCC	1	false
+ACCAAACGTTCTCACC	CDK16	CAGGGACCATAC	1	false
+ACCAAACGTTCTCACC	CELF2	GCAAGGCATTGT	1	false
+ACCAAACGTTCTCACC	CFDP1	GAGTAGTACGAC	1	false
+ACCAAACGTTCTCACC	CIAO1	ATCTTAAAGTAT	1	false
+ACCAAACGTTCTCACC	CREBZF	ATTCACCACCGA	1	false
+ACCAAACGTTCTCACC	CRYM	GCCCATCCCCAG	1	false
+ACCAAACGTTCTCACC	CSMD3	TTTATCGACTAG	1	false
+ACCAAACGTTCTCACC	CTXN1	CCACGCAACTGT	1	false
+ACCAAACGTTCTCACC	CXorf56	ATTTAGTAAATG	1	false
+ACCAAACGTTCTCACC	DAAM1	CATATCTACATG	1	false
+ACCAAACGTTCTCACC	DCLK1	GTCACCTTAGCC	1	false
+ACCAAACGTTCTCACC	DDHD1	AATACGACATTA	1	false
+ACCAAACGTTCTCACC	DDX5	ACTCGAAAGTCC	1	false
+ACCAAACGTTCTCACC	DNAJB14	CGGAATTGATAC	1	false
+ACCAAACGTTCTCACC	DOCK4	TTCATTTCAGGA	1	false
+ACCAAACGTTCTCACC	DOCK7	CGGCTCCGGTCA	1	false
+ACCAAACGTTCTCACC	DOK6	TGCCCTCTCACT	1	false
+ACCAAACGTTCTCACC	EPM2AIP1	TAGACCGTGTTG	1	false
+ACCAAACGTTCTCACC	ETFRF1	ACTACCCCGGGA	1	false
+ACCAAACGTTCTCACC	FANCA	TCACCTGCCTCC	1	false
+ACCAAACGTTCTCACC	FKBP2	GTATCAAATGTA	1	false
+ACCAAACGTTCTCACC	GGA3	TCTCACGGGTTT	1	false
+ACCAAACGTTCTCACC	GNG2	GATTGCACCCAT	1	false
+ACCAAACGTTCTCACC	GPM6A	AAACCCCACGGC	1	false
+ACCAAACGTTCTCACC	GRIN2B	GGCTTTAATTCA	1	false
+ACCAAACGTTCTCACC	GRIN2B	GTTAAACGCATC	1	false
+ACCAAACGTTCTCACC	HAGH	TTTTCAACGCAC	1	false
+ACCAAACGTTCTCACC	KCNIP4-IT1	ACGCATATTCCC	1	false
+ACCAAACGTTCTCACC	KIAA0586	CATCCCCACCCC	1	false
+ACCAAACGTTCTCACC	KIDINS220	TGTTGATCATCT	1	true
+ACCAAACGTTCTCACC	LARS	ACGCACCATCAC	1	false
+ACCAAACGTTCTCACC	LIMCH1	TAGACCTATTGC	1	false
+ACCAAACGTTCTCACC	LINC-PINT	CCCCCCTATCGT	1	false
+ACCAAACGTTCTCACC	LINC01352	TTAGACTGACCA	1	false
+ACCAAACGTTCTCACC	LUC7L3	CGTATCATAACA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACCACAAAATAA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACACATATTTAC	1	false
+ACCAAACGTTCTCACC	MALAT1	GATCTATAGTTC	1	false
+ACCAAACGTTCTCACC	MALAT1	AATCTTTTTCAA	1	true
+ACCAAACGTTCTCACC	MALAT1	TTCGGGTCTAAC	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATATCTGGGC	1	false
+ACCAAACGTTCTCACC	MALAT1	ATTTTAGGATTT	1	true
+ACCAAACGTTCTCACC	MALAT1	GGATAATGAATT	1	false
+ACCAAACGTTCTCACC	MALAT1	TGGCCGACTACA	1	false
+ACCAAACGTTCTCACC	MALAT1	TTTACATGCACA	1	false
+ACCAAACGTTCTCACC	MALAT1	CTTATTAGAATA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATAGTAGATA	1	false
+ACCAAACGTTCTCACC	MALAT1	GATGGAGTATGA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATTAATGAAG	1	false
+ACCAAACGTTCTCACC	MALAT1	ATGATTTCCTAT	1	true
+ACCAAACGTTCTCACC	MALAT1	AAGCTTTTTTCA	1	true
+ACCAAACGTTCTCACC	MALAT1	GTAATCCAGCAC	1	false
+ACCAAACGTTCTCACC	MALAT1	CACTGCTCAACT	1	false
+ACCAAACGTTCTCACC	MALAT1	TTCCTTAGGGCA	1	false
+ACCAAACGTTCTCACC	MALAT1	GGGATTTTACTA	1	false
+ACCAAACGTTCTCACC	MAP1A	CGTTCTAGGAAA	1	false
+ACCAAACGTTCTCACC	MAP1B	CATGGCAATACG	1	false
+ACCAAACGTTCTCACC	MAP4	GCCTGTTAGCAT	1	false
+ACCAAACGTTCTCACC	MAP6	ACACACATCTCT	1	false
+ACCAAACGTTCTCACC	MDM4	TGTACCACTGAT	1	false
+ACCAAACGTTCTCACC	MEG3	GGAATGGAAGTA	1	false
+ACCAAACGTTCTCACC	MEG3	TTCTTCGCATTG	1	true
+ACCAAACGTTCTCACC	MIS18BP1	ACTATCAGCTGT	1	false
+ACCAAACGTTCTCACC	MOG	TATAACATTTGC	1	false
+ACCAAACGTTCTCACC	MPHOSPH8	GGTTCCATAGCC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	AAAAGGCACGGC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TTATTACATAAC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TCTCTCCTCTAT	1	true
+ACCAAACGTTCTCACC	MT-ND5	GTTCATAAGCTG	1	false
+ACCAAACGTTCTCACC	MTX2	TAGCGATTTAAT	1	false
+ACCAAACGTTCTCACC	MYO5A	CCGTCCCGCAGG	1	false
+ACCAAACGTTCTCACC	MYO5C	GACAATAGCCTC	1	false
+ACCAAACGTTCTCACC	NAB1	CTGGTTTTGTTG	1	true
+ACCAAACGTTCTCACC	NBAS	TTCCCGCAAGCT	1	false
+ACCAAACGTTCTCACC	NDFIP1	CTGCCATTATGG	1	false
+ACCAAACGTTCTCACC	NPTN	ATGGATTATAGG	1	false
+ACCAAACGTTCTCACC	NR3C1	GTGTTGTTAATG	1	true
+ACCAAACGTTCTCACC	ORAOV1	GAGTTCCTCGAA	1	false
+ACCAAACGTTCTCACC	PFN2	AACTACTACCTA	1	false
+ACCAAACGTTCTCACC	PGAP1	CAAGTATCCGGC	1	false
+ACCAAACGTTCTCACC	PRKAR1B	CTAAGATTGTTT	1	true
+ACCAAACGTTCTCACC	PRKDC	AGCACCTCAGCT	1	false
+ACCAAACGTTCTCACC	PSIP1	TTTATGAAACGG	1	false
+ACCAAACGTTCTCACC	PSMA1	TCCCGTTACACA	1	false
+ACCAAACGTTCTCACC	PTPN18	AAATTCTAATAC	1	false
+ACCAAACGTTCTCACC	RAP1GAP2	ATGCTCGTCCAG	1	false
+ACCAAACGTTCTCACC	RIMS1	TCTTGGTACAAA	1	false
+ACCAAACGTTCTCACC	RN7SK	TCATTGCTAATT	1	true
+ACCAAACGTTCTCACC	RPL10A	ACGAGTAACATC	1	false
+ACCAAACGTTCTCACC	RPL30	CTGGAAGCGTAA	1	false
+ACCAAACGTTCTCACC	RPL34	TGCACCACAAGG	1	false
+ACCAAACGTTCTCACC	RPLP1	AGAGCTTATCTA	1	false
+ACCAAACGTTCTCACC	RYR2	CAGCAGTCCGTA	1	false
+ACCAAACGTTCTCACC	SAMD8	TCCGCCATATTA	1	false
+ACCAAACGTTCTCACC	SDF4	TTGAGTGTAAGT	1	false
+ACCAAACGTTCTCACC	SH3PXD2A	GATTTGGGGCGT	1	false
+ACCAAACGTTCTCACC	SLC17A7	AATTGATTAAGT	1	false
+ACCAAACGTTCTCACC	SLC26A10	TAGCGTCTTTAG	1	false
+ACCAAACGTTCTCACC	SLC8A1	CCGCATTCCAGG	1	false
+ACCAAACGTTCTCACC	SLC8A1-AS1	CCTTACAGGCAA	1	false
+ACCAAACGTTCTCACC	SLF1	TAATCGTTCGGC	1	false
+ACCAAACGTTCTCACC	SMC1A	CTCATGATTGTT	1	true
+ACCAAACGTTCTCACC	SMURF1	GGCTCCATTGAC	1	false
+ACCAAACGTTCTCACC	SNRNP70	CGAACTTGCTGC	1	false
+ACCAAACGTTCTCACC	SPATA18	CATCAACATCGG	1	false
+ACCAAACGTTCTCACC	SPTBN1	TCTTATGTCTCG	1	true
+ACCAAACGTTCTCACC	SRSF11	TCCAGGCTGCAT	2	false
+ACCAAACGTTCTCACC	SSTR2	AATTGTATCTTA	1	true
+ACCAAACGTTCTCACC	STRN	TGATAGTCCCCG	1	false
+ACCAAACGTTCTCACC	SV2B	TACAAAAATGTT	1	false
+ACCAAACGTTCTCACC	SYNE1	GATTTCTAAGTC	1	false
+ACCAAACGTTCTCACC	TMED4	ACTTCGTGTTCA	1	false
+ACCAAACGTTCTCACC	TMEM117	GGTATGCGTGTA	1	false
+ACCAAACGTTCTCACC	TMEM246	GACATAGCTAAA	1	false
+ACCAAACGTTCTCACC	TMEM87A	TGCCAGCTGACT	1	false
+ACCAAACGTTCTCACC	TMOD2	AATTAAGAGTTA	1	false
+ACCAAACGTTCTCACC	TOMM7	GAATACTCTGGT	1	false
+ACCAAACGTTCTCACC	TRIM27	CCAAGTCCGGAT	1	false
+ACCAAACGTTCTCACC	TRIM44	GATCTGCCCGAC	1	false
+ACCAAACGTTCTCACC	TRIM59	TATATATGCGAT	1	false
+ACCAAACGTTCTCACC	TTC28	ATTCTAGACCCT	1	false
+ACCAAACGTTCTCACC	TTC9B	GCCTCCCTTAGT	1	false
+ACCAAACGTTCTCACC	TVP23A	TTCTCTTTTTCC	1	true
+ACCAAACGTTCTCACC	UNC119	GCCGGAGTTTGC	1	false
+ACCAAACGTTCTCACC	UQCRH	TCACTCATATGT	1	false
+ACCAAACGTTCTCACC	USMG5	ATTTAGTAAATG	1	false
+ACCAAACGTTCTCACC	USP25	AGGACCCGATCA	1	false
+ACCAAACGTTCTCACC	USP25	TGCAGTCCCCGG	1	false
+ACCAAACGTTCTCACC	UTP6	CCCAGGCAGCTA	1	false
+ACCAAACGTTCTCACC	VGLL4	CCGACGGACACA	1	false
+ACCAAACGTTCTCACC	YBEY	TTGCTGGATTTA	1	true
+ACCAAACGTTCTCACC	YEATS2	CTCAACATCATG	1	false
+ACCAAACGTTCTCACC	YWHAH	GATATTGGGTCA	1	false
+ACCAAACGTTCTCACC	ZC2HC1A	AGATGGAAATCC	1	false
+ACCAAACGTTCTCACC	ZFP28	CCTTTTACTGTA	1	true
+ACCAAACGTTCTCACC	ZFYVE16	ATGCAACTTCGG	2	false
+ACCAAACGTTCTCACC	ZNF516	GTGATTGTGCGC	1	false
+ACCAAACGTTCTCACC	ZNF528	CATCCGGACTTA	1	false
+ACCAAACGTTCTCACC	ZRANB3	CTGACTGGATTC	1	false


=====================================
testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.6T.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.both.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.input.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.input2.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.umiReuse.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
testdata/org/broadinstitute/dropseq/barnyard/MarkChimericReads.umiReuse10x.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
testdata/org/broadinstitute/dropseq/barnyard/both.chimeric_read_metrics
=====================================
@@ -0,0 +1,6 @@
+
+## METRICS CLASS	org.broadinstitute.dropseqrna.priv.barnyard.MarkChimericReads$MarkChimericReadMetrics
+NUM_UMIS	NUM_MARKED_UMIS	NUM_T_RICH_UMIS	NUM_REUSED_UMIS
+164	22	20	2
+
+


=====================================
testdata/org/broadinstitute/dropseq/barnyard/both.chimeric_report.txt
=====================================
@@ -0,0 +1,165 @@
+CELL_BARCODE	GENE	MOLECULAR_BARCODE	NUM_OBS	CHIMERIC
+ACCAAACGTTCTCACC	AC025594.3	TACATTACAGCT	1	false
+ACCAAACGTTCTCACC	ACOT13	AGAGTAATATGA	1	false
+ACCAAACGTTCTCACC	AFF4	TAAACTGTTTAA	1	false
+ACCAAACGTTCTCACC	AJAP1	CCGGATTATTGC	1	false
+ACCAAACGTTCTCACC	AL645728.1	CTGCGATTACGG	1	false
+ACCAAACGTTCTCACC	ALDOA	CTTCTGCAATGG	1	false
+ACCAAACGTTCTCACC	ALG1L9P	CCAGCGCTAATT	1	false
+ACCAAACGTTCTCACC	ANKRD10	AATTTTATGAAT	1	true
+ACCAAACGTTCTCACC	ANKRD10-IT1	ATCCTCGTTCTG	1	false
+ACCAAACGTTCTCACC	AP3B2	ACTCGGATACCT	1	false
+ACCAAACGTTCTCACC	APBA2	CATCCTGCGGGC	1	false
+ACCAAACGTTCTCACC	ARGLU1	ACGAGTATTGCC	1	false
+ACCAAACGTTCTCACC	ARHGEF3	TATTTGTCTGAG	1	true
+ACCAAACGTTCTCACC	ARNT2	TGCTATCTTAAC	1	false
+ACCAAACGTTCTCACC	ARPP21	CTGTGTTAATTG	1	true
+ACCAAACGTTCTCACC	ATAD1	AGAAGACGGCCG	1	false
+ACCAAACGTTCTCACC	ATP9B	AGCAAGCACCGA	1	false
+ACCAAACGTTCTCACC	BRD1	GCACTCATTTCG	1	false
+ACCAAACGTTCTCACC	C19orf66	AAAATTTGGCAA	1	false
+ACCAAACGTTCTCACC	CACNA1A	TCACCTCCATAC	1	false
+ACCAAACGTTCTCACC	CAMK1D	ATGATGGTAACA	1	false
+ACCAAACGTTCTCACC	CAPZB	GCATGCTTAGAT	1	false
+ACCAAACGTTCTCACC	CBL	TAACCCTATGAT	1	false
+ACCAAACGTTCTCACC	CCDC3	GACATGGCTCAC	1	false
+ACCAAACGTTCTCACC	CCDC84	TCTCTAGGGTCC	1	false
+ACCAAACGTTCTCACC	CDK16	CAGGGACCATAC	1	false
+ACCAAACGTTCTCACC	CELF2	GCAAGGCATTGT	1	false
+ACCAAACGTTCTCACC	CFDP1	GAGTAGTACGAC	1	false
+ACCAAACGTTCTCACC	CIAO1	ATCTTAAAGTAT	1	false
+ACCAAACGTTCTCACC	CREBZF	ATTCACCACCGA	1	false
+ACCAAACGTTCTCACC	CRYM	GCCCATCCCCAG	1	false
+ACCAAACGTTCTCACC	CSMD3	TTTATCGACTAG	1	false
+ACCAAACGTTCTCACC	CTXN1	CCACGCAACTGT	1	false
+ACCAAACGTTCTCACC	CXorf56	ATTTAGTAAATG	1	true
+ACCAAACGTTCTCACC	DAAM1	CATATCTACATG	1	false
+ACCAAACGTTCTCACC	DCLK1	GTCACCTTAGCC	1	false
+ACCAAACGTTCTCACC	DDHD1	AATACGACATTA	1	false
+ACCAAACGTTCTCACC	DDX5	ACTCGAAAGTCC	1	false
+ACCAAACGTTCTCACC	DNAJB14	CGGAATTGATAC	1	false
+ACCAAACGTTCTCACC	DOCK4	TTCATTTCAGGA	1	false
+ACCAAACGTTCTCACC	DOCK7	CGGCTCCGGTCA	1	false
+ACCAAACGTTCTCACC	DOK6	TGCCCTCTCACT	1	false
+ACCAAACGTTCTCACC	EPM2AIP1	TAGACCGTGTTG	1	false
+ACCAAACGTTCTCACC	ETFRF1	ACTACCCCGGGA	1	false
+ACCAAACGTTCTCACC	FANCA	TCACCTGCCTCC	1	false
+ACCAAACGTTCTCACC	FKBP2	GTATCAAATGTA	1	false
+ACCAAACGTTCTCACC	GGA3	TCTCACGGGTTT	1	false
+ACCAAACGTTCTCACC	GNG2	GATTGCACCCAT	1	false
+ACCAAACGTTCTCACC	GPM6A	AAACCCCACGGC	1	false
+ACCAAACGTTCTCACC	GRIN2B	GGCTTTAATTCA	1	false
+ACCAAACGTTCTCACC	GRIN2B	GTTAAACGCATC	1	false
+ACCAAACGTTCTCACC	HAGH	TTTTCAACGCAC	1	false
+ACCAAACGTTCTCACC	KCNIP4-IT1	ACGCATATTCCC	1	false
+ACCAAACGTTCTCACC	KIAA0586	CATCCCCACCCC	1	false
+ACCAAACGTTCTCACC	KIDINS220	TGTTGATCATCT	1	true
+ACCAAACGTTCTCACC	LARS	ACGCACCATCAC	1	false
+ACCAAACGTTCTCACC	LIMCH1	TAGACCTATTGC	1	false
+ACCAAACGTTCTCACC	LINC-PINT	CCCCCCTATCGT	1	false
+ACCAAACGTTCTCACC	LINC01352	TTAGACTGACCA	1	false
+ACCAAACGTTCTCACC	LUC7L3	CGTATCATAACA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACCACAAAATAA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACACATATTTAC	1	false
+ACCAAACGTTCTCACC	MALAT1	GATCTATAGTTC	1	false
+ACCAAACGTTCTCACC	MALAT1	AATCTTTTTCAA	1	true
+ACCAAACGTTCTCACC	MALAT1	TTCGGGTCTAAC	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATATCTGGGC	1	false
+ACCAAACGTTCTCACC	MALAT1	ATTTTAGGATTT	1	true
+ACCAAACGTTCTCACC	MALAT1	GGATAATGAATT	1	false
+ACCAAACGTTCTCACC	MALAT1	TGGCCGACTACA	1	false
+ACCAAACGTTCTCACC	MALAT1	TTTACATGCACA	1	false
+ACCAAACGTTCTCACC	MALAT1	CTTATTAGAATA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATAGTAGATA	1	false
+ACCAAACGTTCTCACC	MALAT1	GATGGAGTATGA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATTAATGAAG	1	false
+ACCAAACGTTCTCACC	MALAT1	ATGATTTCCTAT	1	true
+ACCAAACGTTCTCACC	MALAT1	AAGCTTTTTTCA	1	true
+ACCAAACGTTCTCACC	MALAT1	GTAATCCAGCAC	1	false
+ACCAAACGTTCTCACC	MALAT1	CACTGCTCAACT	1	false
+ACCAAACGTTCTCACC	MALAT1	TTCCTTAGGGCA	1	false
+ACCAAACGTTCTCACC	MALAT1	GGGATTTTACTA	1	false
+ACCAAACGTTCTCACC	MAP1A	CGTTCTAGGAAA	1	false
+ACCAAACGTTCTCACC	MAP1B	CATGGCAATACG	1	false
+ACCAAACGTTCTCACC	MAP4	GCCTGTTAGCAT	1	false
+ACCAAACGTTCTCACC	MAP6	ACACACATCTCT	1	false
+ACCAAACGTTCTCACC	MDM4	TGTACCACTGAT	1	false
+ACCAAACGTTCTCACC	MEG3	GGAATGGAAGTA	1	false
+ACCAAACGTTCTCACC	MEG3	TTCTTCGCATTG	1	true
+ACCAAACGTTCTCACC	MIS18BP1	ACTATCAGCTGT	1	false
+ACCAAACGTTCTCACC	MOG	TATAACATTTGC	1	false
+ACCAAACGTTCTCACC	MPHOSPH8	GGTTCCATAGCC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	AAAAGGCACGGC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TTATTACATAAC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TCTCTCCTCTAT	1	true
+ACCAAACGTTCTCACC	MT-ND5	GTTCATAAGCTG	1	false
+ACCAAACGTTCTCACC	MTX2	TAGCGATTTAAT	1	false
+ACCAAACGTTCTCACC	MYO5A	CCGTCCCGCAGG	1	false
+ACCAAACGTTCTCACC	MYO5C	GACAATAGCCTC	1	false
+ACCAAACGTTCTCACC	NAB1	CTGGTTTTGTTG	1	true
+ACCAAACGTTCTCACC	NBAS	TTCCCGCAAGCT	1	false
+ACCAAACGTTCTCACC	NDFIP1	CTGCCATTATGG	1	false
+ACCAAACGTTCTCACC	NPTN	ATGGATTATAGG	1	false
+ACCAAACGTTCTCACC	NR3C1	GTGTTGTTAATG	1	true
+ACCAAACGTTCTCACC	ORAOV1	GAGTTCCTCGAA	1	false
+ACCAAACGTTCTCACC	PFN2	AACTACTACCTA	1	false
+ACCAAACGTTCTCACC	PGAP1	CAAGTATCCGGC	1	false
+ACCAAACGTTCTCACC	PRKAR1B	CTAAGATTGTTT	1	true
+ACCAAACGTTCTCACC	PRKDC	AGCACCTCAGCT	1	false
+ACCAAACGTTCTCACC	PSIP1	TTTATGAAACGG	1	false
+ACCAAACGTTCTCACC	PSMA1	TCCCGTTACACA	1	false
+ACCAAACGTTCTCACC	PTPN18	AAATTCTAATAC	1	false
+ACCAAACGTTCTCACC	RAP1GAP2	ATGCTCGTCCAG	1	false
+ACCAAACGTTCTCACC	RIMS1	TCTTGGTACAAA	1	false
+ACCAAACGTTCTCACC	RN7SK	TCATTGCTAATT	1	true
+ACCAAACGTTCTCACC	RPL10A	ACGAGTAACATC	1	false
+ACCAAACGTTCTCACC	RPL30	CTGGAAGCGTAA	1	false
+ACCAAACGTTCTCACC	RPL34	TGCACCACAAGG	1	false
+ACCAAACGTTCTCACC	RPLP1	AGAGCTTATCTA	1	false
+ACCAAACGTTCTCACC	RYR2	CAGCAGTCCGTA	1	false
+ACCAAACGTTCTCACC	SAMD8	TCCGCCATATTA	1	false
+ACCAAACGTTCTCACC	SDF4	TTGAGTGTAAGT	1	false
+ACCAAACGTTCTCACC	SH3PXD2A	GATTTGGGGCGT	1	false
+ACCAAACGTTCTCACC	SLC17A7	AATTGATTAAGT	1	false
+ACCAAACGTTCTCACC	SLC26A10	TAGCGTCTTTAG	1	false
+ACCAAACGTTCTCACC	SLC8A1	CCGCATTCCAGG	1	false
+ACCAAACGTTCTCACC	SLC8A1-AS1	CCTTACAGGCAA	1	false
+ACCAAACGTTCTCACC	SLF1	TAATCGTTCGGC	1	false
+ACCAAACGTTCTCACC	SMC1A	CTCATGATTGTT	1	true
+ACCAAACGTTCTCACC	SMURF1	GGCTCCATTGAC	1	false
+ACCAAACGTTCTCACC	SNRNP70	CGAACTTGCTGC	1	false
+ACCAAACGTTCTCACC	SPATA18	CATCAACATCGG	1	false
+ACCAAACGTTCTCACC	SPTBN1	TCTTATGTCTCG	1	true
+ACCAAACGTTCTCACC	SRSF11	TCCAGGCTGCAT	2	false
+ACCAAACGTTCTCACC	SSTR2	AATTGTATCTTA	1	true
+ACCAAACGTTCTCACC	STRN	TGATAGTCCCCG	1	false
+ACCAAACGTTCTCACC	SV2B	TACAAAAATGTT	1	false
+ACCAAACGTTCTCACC	SYNE1	GATTTCTAAGTC	1	false
+ACCAAACGTTCTCACC	TMED4	ACTTCGTGTTCA	1	false
+ACCAAACGTTCTCACC	TMEM117	GGTATGCGTGTA	1	false
+ACCAAACGTTCTCACC	TMEM246	GACATAGCTAAA	1	false
+ACCAAACGTTCTCACC	TMEM87A	TGCCAGCTGACT	1	false
+ACCAAACGTTCTCACC	TMOD2	AATTAAGAGTTA	1	false
+ACCAAACGTTCTCACC	TOMM7	GAATACTCTGGT	1	false
+ACCAAACGTTCTCACC	TRIM27	CCAAGTCCGGAT	1	false
+ACCAAACGTTCTCACC	TRIM44	GATCTGCCCGAC	1	false
+ACCAAACGTTCTCACC	TRIM59	TATATATGCGAT	1	false
+ACCAAACGTTCTCACC	TTC28	ATTCTAGACCCT	1	false
+ACCAAACGTTCTCACC	TTC9B	GCCTCCCTTAGT	1	false
+ACCAAACGTTCTCACC	TVP23A	TTCTCTTTTTCC	1	true
+ACCAAACGTTCTCACC	UNC119	GCCGGAGTTTGC	1	false
+ACCAAACGTTCTCACC	UQCRH	TCACTCATATGT	1	false
+ACCAAACGTTCTCACC	USMG5	ATTTAGTAAATG	1	true
+ACCAAACGTTCTCACC	USP25	AGGACCCGATCA	1	false
+ACCAAACGTTCTCACC	USP25	TGCAGTCCCCGG	1	false
+ACCAAACGTTCTCACC	UTP6	CCCAGGCAGCTA	1	false
+ACCAAACGTTCTCACC	VGLL4	CCGACGGACACA	1	false
+ACCAAACGTTCTCACC	YBEY	TTGCTGGATTTA	1	true
+ACCAAACGTTCTCACC	YEATS2	CTCAACATCATG	1	false
+ACCAAACGTTCTCACC	YWHAH	GATATTGGGTCA	1	false
+ACCAAACGTTCTCACC	ZC2HC1A	AGATGGAAATCC	1	false
+ACCAAACGTTCTCACC	ZFP28	CCTTTTACTGTA	1	true
+ACCAAACGTTCTCACC	ZFYVE16	ATGCAACTTCGG	2	false
+ACCAAACGTTCTCACC	ZNF516	GTGATTGTGCGC	1	false
+ACCAAACGTTCTCACC	ZNF528	CATCCGGACTTA	1	false
+ACCAAACGTTCTCACC	ZRANB3	CTGACTGGATTC	1	false


=====================================
testdata/org/broadinstitute/dropseq/barnyard/ed_collapse.chimeric_report.txt
=====================================
@@ -0,0 +1,3 @@
+CELL_BARCODE	GENE	MOLECULAR_BARCODE	NUM_OBS	CHIMERIC
+AAAAGGTTATGT	AC018832.1	CCTAGGGG	18	false
+AAAAGGTTATGT	AC018832.1	CCTAGGGT	1	true


=====================================
testdata/org/broadinstitute/dropseq/barnyard/selectedCellBarcodes.txt
=====================================
@@ -0,0 +1 @@
+ACCAAACGTTCTCACC


=====================================
testdata/org/broadinstitute/dropseq/barnyard/two_cells.chimeric_report.txt
=====================================
@@ -0,0 +1,3 @@
+CELL_BARCODE	GENE	MOLECULAR_BARCODE	NUM_OBS	CHIMERIC
+ACCAAACGTTCTCACC	AC025594.3	TACATTACAGCT	1	false
+ACGTAACGTTCTCACC	ACOT13	AGAGTAATATGA	1	false


=====================================
testdata/org/broadinstitute/dropseq/barnyard/umiReuse.chimeric_read_metrics
=====================================
@@ -0,0 +1,6 @@
+
+## METRICS CLASS	org.broadinstitute.dropseqrna.priv.barnyard.MarkChimericReads$MarkChimericReadMetrics
+NUM_UMIS	NUM_MARKED_UMIS	NUM_T_RICH_UMIS	NUM_REUSED_UMIS
+164	2	0	2
+
+


=====================================
testdata/org/broadinstitute/dropseq/barnyard/umiReuse.chimeric_report.txt
=====================================
@@ -0,0 +1,165 @@
+CELL_BARCODE	GENE	MOLECULAR_BARCODE	NUM_OBS	CHIMERIC
+ACCAAACGTTCTCACC	AC025594.3	TACATTACAGCT	1	false
+ACCAAACGTTCTCACC	ACOT13	AGAGTAATATGA	1	false
+ACCAAACGTTCTCACC	AFF4	TAAACTGTTTAA	1	false
+ACCAAACGTTCTCACC	AJAP1	CCGGATTATTGC	1	false
+ACCAAACGTTCTCACC	AL645728.1	CTGCGATTACGG	1	false
+ACCAAACGTTCTCACC	ALDOA	CTTCTGCAATGG	1	false
+ACCAAACGTTCTCACC	ALG1L9P	CCAGCGCTAATT	1	false
+ACCAAACGTTCTCACC	ANKRD10	AATTTTATGAAT	1	false
+ACCAAACGTTCTCACC	ANKRD10-IT1	ATCCTCGTTCTG	1	false
+ACCAAACGTTCTCACC	AP3B2	ACTCGGATACCT	1	false
+ACCAAACGTTCTCACC	APBA2	CATCCTGCGGGC	1	false
+ACCAAACGTTCTCACC	ARGLU1	ACGAGTATTGCC	1	false
+ACCAAACGTTCTCACC	ARHGEF3	TATTTGTCTGAG	1	false
+ACCAAACGTTCTCACC	ARNT2	TGCTATCTTAAC	1	false
+ACCAAACGTTCTCACC	ARPP21	CTGTGTTAATTG	1	false
+ACCAAACGTTCTCACC	ATAD1	AGAAGACGGCCG	1	false
+ACCAAACGTTCTCACC	ATP9B	AGCAAGCACCGA	1	false
+ACCAAACGTTCTCACC	BRD1	GCACTCATTTCG	1	false
+ACCAAACGTTCTCACC	C19orf66	AAAATTTGGCAA	1	false
+ACCAAACGTTCTCACC	CACNA1A	TCACCTCCATAC	1	false
+ACCAAACGTTCTCACC	CAMK1D	ATGATGGTAACA	1	false
+ACCAAACGTTCTCACC	CAPZB	GCATGCTTAGAT	1	false
+ACCAAACGTTCTCACC	CBL	TAACCCTATGAT	1	false
+ACCAAACGTTCTCACC	CCDC3	GACATGGCTCAC	1	false
+ACCAAACGTTCTCACC	CCDC84	TCTCTAGGGTCC	1	false
+ACCAAACGTTCTCACC	CDK16	CAGGGACCATAC	1	false
+ACCAAACGTTCTCACC	CELF2	GCAAGGCATTGT	1	false
+ACCAAACGTTCTCACC	CFDP1	GAGTAGTACGAC	1	false
+ACCAAACGTTCTCACC	CIAO1	ATCTTAAAGTAT	1	false
+ACCAAACGTTCTCACC	CREBZF	ATTCACCACCGA	1	false
+ACCAAACGTTCTCACC	CRYM	GCCCATCCCCAG	1	false
+ACCAAACGTTCTCACC	CSMD3	TTTATCGACTAG	1	false
+ACCAAACGTTCTCACC	CTXN1	CCACGCAACTGT	1	false
+ACCAAACGTTCTCACC	CXorf56	ATTTAGTAAATG	1	true
+ACCAAACGTTCTCACC	DAAM1	CATATCTACATG	1	false
+ACCAAACGTTCTCACC	DCLK1	GTCACCTTAGCC	1	false
+ACCAAACGTTCTCACC	DDHD1	AATACGACATTA	1	false
+ACCAAACGTTCTCACC	DDX5	ACTCGAAAGTCC	1	false
+ACCAAACGTTCTCACC	DNAJB14	CGGAATTGATAC	1	false
+ACCAAACGTTCTCACC	DOCK4	TTCATTTCAGGA	1	false
+ACCAAACGTTCTCACC	DOCK7	CGGCTCCGGTCA	1	false
+ACCAAACGTTCTCACC	DOK6	TGCCCTCTCACT	1	false
+ACCAAACGTTCTCACC	EPM2AIP1	TAGACCGTGTTG	1	false
+ACCAAACGTTCTCACC	ETFRF1	ACTACCCCGGGA	1	false
+ACCAAACGTTCTCACC	FANCA	TCACCTGCCTCC	1	false
+ACCAAACGTTCTCACC	FKBP2	GTATCAAATGTA	1	false
+ACCAAACGTTCTCACC	GGA3	TCTCACGGGTTT	1	false
+ACCAAACGTTCTCACC	GNG2	GATTGCACCCAT	1	false
+ACCAAACGTTCTCACC	GPM6A	AAACCCCACGGC	1	false
+ACCAAACGTTCTCACC	GRIN2B	GGCTTTAATTCA	1	false
+ACCAAACGTTCTCACC	GRIN2B	GTTAAACGCATC	1	false
+ACCAAACGTTCTCACC	HAGH	TTTTCAACGCAC	1	false
+ACCAAACGTTCTCACC	KCNIP4-IT1	ACGCATATTCCC	1	false
+ACCAAACGTTCTCACC	KIAA0586	CATCCCCACCCC	1	false
+ACCAAACGTTCTCACC	KIDINS220	TGTTGATCATCT	1	false
+ACCAAACGTTCTCACC	LARS	ACGCACCATCAC	1	false
+ACCAAACGTTCTCACC	LIMCH1	TAGACCTATTGC	1	false
+ACCAAACGTTCTCACC	LINC-PINT	CCCCCCTATCGT	1	false
+ACCAAACGTTCTCACC	LINC01352	TTAGACTGACCA	1	false
+ACCAAACGTTCTCACC	LUC7L3	CGTATCATAACA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACCACAAAATAA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACACATATTTAC	1	false
+ACCAAACGTTCTCACC	MALAT1	GATCTATAGTTC	1	false
+ACCAAACGTTCTCACC	MALAT1	AATCTTTTTCAA	1	false
+ACCAAACGTTCTCACC	MALAT1	TTCGGGTCTAAC	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATATCTGGGC	1	false
+ACCAAACGTTCTCACC	MALAT1	ATTTTAGGATTT	1	false
+ACCAAACGTTCTCACC	MALAT1	GGATAATGAATT	1	false
+ACCAAACGTTCTCACC	MALAT1	TGGCCGACTACA	1	false
+ACCAAACGTTCTCACC	MALAT1	TTTACATGCACA	1	false
+ACCAAACGTTCTCACC	MALAT1	CTTATTAGAATA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATAGTAGATA	1	false
+ACCAAACGTTCTCACC	MALAT1	GATGGAGTATGA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATTAATGAAG	1	false
+ACCAAACGTTCTCACC	MALAT1	ATGATTTCCTAT	1	false
+ACCAAACGTTCTCACC	MALAT1	AAGCTTTTTTCA	1	false
+ACCAAACGTTCTCACC	MALAT1	GTAATCCAGCAC	1	false
+ACCAAACGTTCTCACC	MALAT1	CACTGCTCAACT	1	false
+ACCAAACGTTCTCACC	MALAT1	TTCCTTAGGGCA	1	false
+ACCAAACGTTCTCACC	MALAT1	GGGATTTTACTA	1	false
+ACCAAACGTTCTCACC	MAP1A	CGTTCTAGGAAA	1	false
+ACCAAACGTTCTCACC	MAP1B	CATGGCAATACG	1	false
+ACCAAACGTTCTCACC	MAP4	GCCTGTTAGCAT	1	false
+ACCAAACGTTCTCACC	MAP6	ACACACATCTCT	1	false
+ACCAAACGTTCTCACC	MDM4	TGTACCACTGAT	1	false
+ACCAAACGTTCTCACC	MEG3	GGAATGGAAGTA	1	false
+ACCAAACGTTCTCACC	MEG3	TTCTTCGCATTG	1	false
+ACCAAACGTTCTCACC	MIS18BP1	ACTATCAGCTGT	1	false
+ACCAAACGTTCTCACC	MOG	TATAACATTTGC	1	false
+ACCAAACGTTCTCACC	MPHOSPH8	GGTTCCATAGCC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	AAAAGGCACGGC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TTATTACATAAC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TCTCTCCTCTAT	1	false
+ACCAAACGTTCTCACC	MT-ND5	GTTCATAAGCTG	1	false
+ACCAAACGTTCTCACC	MTX2	TAGCGATTTAAT	1	false
+ACCAAACGTTCTCACC	MYO5A	CCGTCCCGCAGG	1	false
+ACCAAACGTTCTCACC	MYO5C	GACAATAGCCTC	1	false
+ACCAAACGTTCTCACC	NAB1	CTGGTTTTGTTG	1	false
+ACCAAACGTTCTCACC	NBAS	TTCCCGCAAGCT	1	false
+ACCAAACGTTCTCACC	NDFIP1	CTGCCATTATGG	1	false
+ACCAAACGTTCTCACC	NPTN	ATGGATTATAGG	1	false
+ACCAAACGTTCTCACC	NR3C1	GTGTTGTTAATG	1	false
+ACCAAACGTTCTCACC	ORAOV1	GAGTTCCTCGAA	1	false
+ACCAAACGTTCTCACC	PFN2	AACTACTACCTA	1	false
+ACCAAACGTTCTCACC	PGAP1	CAAGTATCCGGC	1	false
+ACCAAACGTTCTCACC	PRKAR1B	CTAAGATTGTTT	1	false
+ACCAAACGTTCTCACC	PRKDC	AGCACCTCAGCT	1	false
+ACCAAACGTTCTCACC	PSIP1	TTTATGAAACGG	1	false
+ACCAAACGTTCTCACC	PSMA1	TCCCGTTACACA	1	false
+ACCAAACGTTCTCACC	PTPN18	AAATTCTAATAC	1	false
+ACCAAACGTTCTCACC	RAP1GAP2	ATGCTCGTCCAG	1	false
+ACCAAACGTTCTCACC	RIMS1	TCTTGGTACAAA	1	false
+ACCAAACGTTCTCACC	RN7SK	TCATTGCTAATT	1	false
+ACCAAACGTTCTCACC	RPL10A	ACGAGTAACATC	1	false
+ACCAAACGTTCTCACC	RPL30	CTGGAAGCGTAA	1	false
+ACCAAACGTTCTCACC	RPL34	TGCACCACAAGG	1	false
+ACCAAACGTTCTCACC	RPLP1	AGAGCTTATCTA	1	false
+ACCAAACGTTCTCACC	RYR2	CAGCAGTCCGTA	1	false
+ACCAAACGTTCTCACC	SAMD8	TCCGCCATATTA	1	false
+ACCAAACGTTCTCACC	SDF4	TTGAGTGTAAGT	1	false
+ACCAAACGTTCTCACC	SH3PXD2A	GATTTGGGGCGT	1	false
+ACCAAACGTTCTCACC	SLC17A7	AATTGATTAAGT	1	false
+ACCAAACGTTCTCACC	SLC26A10	TAGCGTCTTTAG	1	false
+ACCAAACGTTCTCACC	SLC8A1	CCGCATTCCAGG	1	false
+ACCAAACGTTCTCACC	SLC8A1-AS1	CCTTACAGGCAA	1	false
+ACCAAACGTTCTCACC	SLF1	TAATCGTTCGGC	1	false
+ACCAAACGTTCTCACC	SMC1A	CTCATGATTGTT	1	false
+ACCAAACGTTCTCACC	SMURF1	GGCTCCATTGAC	1	false
+ACCAAACGTTCTCACC	SNRNP70	CGAACTTGCTGC	1	false
+ACCAAACGTTCTCACC	SPATA18	CATCAACATCGG	1	false
+ACCAAACGTTCTCACC	SPTBN1	TCTTATGTCTCG	1	false
+ACCAAACGTTCTCACC	SRSF11	TCCAGGCTGCAT	2	false
+ACCAAACGTTCTCACC	SSTR2	AATTGTATCTTA	1	false
+ACCAAACGTTCTCACC	STRN	TGATAGTCCCCG	1	false
+ACCAAACGTTCTCACC	SV2B	TACAAAAATGTT	1	false
+ACCAAACGTTCTCACC	SYNE1	GATTTCTAAGTC	1	false
+ACCAAACGTTCTCACC	TMED4	ACTTCGTGTTCA	1	false
+ACCAAACGTTCTCACC	TMEM117	GGTATGCGTGTA	1	false
+ACCAAACGTTCTCACC	TMEM246	GACATAGCTAAA	1	false
+ACCAAACGTTCTCACC	TMEM87A	TGCCAGCTGACT	1	false
+ACCAAACGTTCTCACC	TMOD2	AATTAAGAGTTA	1	false
+ACCAAACGTTCTCACC	TOMM7	GAATACTCTGGT	1	false
+ACCAAACGTTCTCACC	TRIM27	CCAAGTCCGGAT	1	false
+ACCAAACGTTCTCACC	TRIM44	GATCTGCCCGAC	1	false
+ACCAAACGTTCTCACC	TRIM59	TATATATGCGAT	1	false
+ACCAAACGTTCTCACC	TTC28	ATTCTAGACCCT	1	false
+ACCAAACGTTCTCACC	TTC9B	GCCTCCCTTAGT	1	false
+ACCAAACGTTCTCACC	TVP23A	TTCTCTTTTTCC	1	false
+ACCAAACGTTCTCACC	UNC119	GCCGGAGTTTGC	1	false
+ACCAAACGTTCTCACC	UQCRH	TCACTCATATGT	1	false
+ACCAAACGTTCTCACC	USMG5	ATTTAGTAAATG	1	true
+ACCAAACGTTCTCACC	USP25	AGGACCCGATCA	1	false
+ACCAAACGTTCTCACC	USP25	TGCAGTCCCCGG	1	false
+ACCAAACGTTCTCACC	UTP6	CCCAGGCAGCTA	1	false
+ACCAAACGTTCTCACC	VGLL4	CCGACGGACACA	1	false
+ACCAAACGTTCTCACC	YBEY	TTGCTGGATTTA	1	false
+ACCAAACGTTCTCACC	YEATS2	CTCAACATCATG	1	false
+ACCAAACGTTCTCACC	YWHAH	GATATTGGGTCA	1	false
+ACCAAACGTTCTCACC	ZC2HC1A	AGATGGAAATCC	1	false
+ACCAAACGTTCTCACC	ZFP28	CCTTTTACTGTA	1	false
+ACCAAACGTTCTCACC	ZFYVE16	ATGCAACTTCGG	2	false
+ACCAAACGTTCTCACC	ZNF516	GTGATTGTGCGC	1	false
+ACCAAACGTTCTCACC	ZNF528	CATCCGGACTTA	1	false
+ACCAAACGTTCTCACC	ZRANB3	CTGACTGGATTC	1	false


=====================================
testdata/org/broadinstitute/dropseq/barnyard/umiReuse10x.chimeric_read_metrics
=====================================
@@ -0,0 +1,6 @@
+
+## METRICS CLASS	org.broadinstitute.dropseqrna.priv.barnyard.MarkChimericReads$MarkChimericReadMetrics
+NUM_UMIS	NUM_MARKED_UMIS	NUM_T_RICH_UMIS	NUM_REUSED_UMIS
+164	1	0	1	
+
+


=====================================
testdata/org/broadinstitute/dropseq/barnyard/umiReuse10x.chimeric_report.txt
=====================================
@@ -0,0 +1,165 @@
+CELL_BARCODE	GENE	MOLECULAR_BARCODE	NUM_OBS	CHIMERIC
+ACCAAACGTTCTCACC	AC025594.3	TACATTACAGCT	1	false
+ACCAAACGTTCTCACC	ACOT13	AGAGTAATATGA	1	false
+ACCAAACGTTCTCACC	AFF4	TAAACTGTTTAA	1	false
+ACCAAACGTTCTCACC	AJAP1	CCGGATTATTGC	1	false
+ACCAAACGTTCTCACC	AL645728.1	CTGCGATTACGG	1	false
+ACCAAACGTTCTCACC	ALDOA	CTTCTGCAATGG	1	false
+ACCAAACGTTCTCACC	ALG1L9P	CCAGCGCTAATT	1	false
+ACCAAACGTTCTCACC	ANKRD10	AATTTTATGAAT	1	false
+ACCAAACGTTCTCACC	ANKRD10-IT1	ATCCTCGTTCTG	1	false
+ACCAAACGTTCTCACC	AP3B2	ACTCGGATACCT	1	false
+ACCAAACGTTCTCACC	APBA2	CATCCTGCGGGC	1	false
+ACCAAACGTTCTCACC	ARGLU1	ACGAGTATTGCC	1	false
+ACCAAACGTTCTCACC	ARHGEF3	TATTTGTCTGAG	1	false
+ACCAAACGTTCTCACC	ARNT2	TGCTATCTTAAC	1	false
+ACCAAACGTTCTCACC	ARPP21	CTGTGTTAATTG	1	false
+ACCAAACGTTCTCACC	ATAD1	AGAAGACGGCCG	1	false
+ACCAAACGTTCTCACC	ATP9B	AGCAAGCACCGA	1	false
+ACCAAACGTTCTCACC	BRD1	GCACTCATTTCG	1	false
+ACCAAACGTTCTCACC	C19orf66	AAAATTTGGCAA	1	false
+ACCAAACGTTCTCACC	CACNA1A	TCACCTCCATAC	1	false
+ACCAAACGTTCTCACC	CAMK1D	ATGATGGTAACA	1	false
+ACCAAACGTTCTCACC	CAPZB	GCATGCTTAGAT	1	false
+ACCAAACGTTCTCACC	CBL	TAACCCTATGAT	1	false
+ACCAAACGTTCTCACC	CCDC3	GACATGGCTCAC	1	false
+ACCAAACGTTCTCACC	CCDC84	TCTCTAGGGTCC	1	false
+ACCAAACGTTCTCACC	CDK16	CAGGGACCATAC	1	false
+ACCAAACGTTCTCACC	CELF2	GCAAGGCATTGT	1	false
+ACCAAACGTTCTCACC	CFDP1	GAGTAGTACGAC	1	false
+ACCAAACGTTCTCACC	CIAO1	ATCTTAAAGTAT	1	false
+ACCAAACGTTCTCACC	CREBZF	ATTCACCACCGA	1	false
+ACCAAACGTTCTCACC	CRYM	GCCCATCCCCAG	1	false
+ACCAAACGTTCTCACC	CSMD3	TTTATCGACTAG	1	false
+ACCAAACGTTCTCACC	CTXN1	CCACGCAACTGT	1	false
+ACCAAACGTTCTCACC	CXorf56	ATTTAGTAAATG	1	true
+ACCAAACGTTCTCACC	DAAM1	CATATCTACATG	1	false
+ACCAAACGTTCTCACC	DCLK1	GTCACCTTAGCC	1	false
+ACCAAACGTTCTCACC	DDHD1	AATACGACATTA	1	false
+ACCAAACGTTCTCACC	DDX5	ACTCGAAAGTCC	1	false
+ACCAAACGTTCTCACC	DNAJB14	CGGAATTGATAC	1	false
+ACCAAACGTTCTCACC	DOCK4	TTCATTTCAGGA	1	false
+ACCAAACGTTCTCACC	DOCK7	CGGCTCCGGTCA	1	false
+ACCAAACGTTCTCACC	DOK6	TGCCCTCTCACT	1	false
+ACCAAACGTTCTCACC	EPM2AIP1	TAGACCGTGTTG	1	false
+ACCAAACGTTCTCACC	ETFRF1	ACTACCCCGGGA	1	false
+ACCAAACGTTCTCACC	FANCA	TCACCTGCCTCC	1	false
+ACCAAACGTTCTCACC	FKBP2	GTATCAAATGTA	1	false
+ACCAAACGTTCTCACC	GGA3	TCTCACGGGTTT	1	false
+ACCAAACGTTCTCACC	GNG2	GATTGCACCCAT	1	false
+ACCAAACGTTCTCACC	GPM6A	AAACCCCACGGC	1	false
+ACCAAACGTTCTCACC	GRIN2B	GGCTTTAATTCA	1	false
+ACCAAACGTTCTCACC	GRIN2B	GTTAAACGCATC	1	false
+ACCAAACGTTCTCACC	HAGH	TTTTCAACGCAC	1	false
+ACCAAACGTTCTCACC	KCNIP4-IT1	ACGCATATTCCC	1	false
+ACCAAACGTTCTCACC	KIAA0586	CATCCCCACCCC	1	false
+ACCAAACGTTCTCACC	KIDINS220	TGTTGATCATCT	1	false
+ACCAAACGTTCTCACC	LARS	ACGCACCATCAC	1	false
+ACCAAACGTTCTCACC	LIMCH1	TAGACCTATTGC	1	false
+ACCAAACGTTCTCACC	LINC-PINT	CCCCCCTATCGT	1	false
+ACCAAACGTTCTCACC	LINC01352	TTAGACTGACCA	1	false
+ACCAAACGTTCTCACC	LUC7L3	CGTATCATAACA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACCACAAAATAA	1	false
+ACCAAACGTTCTCACC	MALAT1	ACACATATTTAC	1	false
+ACCAAACGTTCTCACC	MALAT1	GATCTATAGTTC	1	false
+ACCAAACGTTCTCACC	MALAT1	AATCTTTTTCAA	1	false
+ACCAAACGTTCTCACC	MALAT1	TTCGGGTCTAAC	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATATCTGGGC	1	false
+ACCAAACGTTCTCACC	MALAT1	ATTTTAGGATTT	1	false
+ACCAAACGTTCTCACC	MALAT1	GGATAATGAATT	1	false
+ACCAAACGTTCTCACC	MALAT1	TGGCCGACTACA	1	false
+ACCAAACGTTCTCACC	MALAT1	TTTACATGCACA	1	false
+ACCAAACGTTCTCACC	MALAT1	CTTATTAGAATA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATAGTAGATA	1	false
+ACCAAACGTTCTCACC	MALAT1	GATGGAGTATGA	1	false
+ACCAAACGTTCTCACC	MALAT1	AAATTAATGAAG	1	false
+ACCAAACGTTCTCACC	MALAT1	ATGATTTCCTAT	1	false
+ACCAAACGTTCTCACC	MALAT1	AAGCTTTTTTCA	1	false
+ACCAAACGTTCTCACC	MALAT1	GTAATCCAGCAC	1	false
+ACCAAACGTTCTCACC	MALAT1	CACTGCTCAACT	1	false
+ACCAAACGTTCTCACC	MALAT1	TTCCTTAGGGCA	1	false
+ACCAAACGTTCTCACC	MALAT1	GGGATTTTACTA	1	false
+ACCAAACGTTCTCACC	MAP1A	CGTTCTAGGAAA	1	false
+ACCAAACGTTCTCACC	MAP1B	CATGGCAATACG	1	false
+ACCAAACGTTCTCACC	MAP4	GCCTGTTAGCAT	1	false
+ACCAAACGTTCTCACC	MAP6	ACACACATCTCT	1	false
+ACCAAACGTTCTCACC	MDM4	TGTACCACTGAT	1	false
+ACCAAACGTTCTCACC	MEG3	GGAATGGAAGTA	1	false
+ACCAAACGTTCTCACC	MEG3	TTCTTCGCATTG	1	false
+ACCAAACGTTCTCACC	MIS18BP1	ACTATCAGCTGT	1	false
+ACCAAACGTTCTCACC	MOG	TATAACATTTGC	1	false
+ACCAAACGTTCTCACC	MPHOSPH8	GGTTCCATAGCC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	AAAAGGCACGGC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TTATTACATAAC	1	false
+ACCAAACGTTCTCACC	MT-ATP6	TCTCTCCTCTAT	1	false
+ACCAAACGTTCTCACC	MT-ND5	GTTCATAAGCTG	1	false
+ACCAAACGTTCTCACC	MTX2	TAGCGATTTAAT	1	false
+ACCAAACGTTCTCACC	MYO5A	CCGTCCCGCAGG	1	false
+ACCAAACGTTCTCACC	MYO5C	GACAATAGCCTC	1	false
+ACCAAACGTTCTCACC	NAB1	CTGGTTTTGTTG	1	false
+ACCAAACGTTCTCACC	NBAS	TTCCCGCAAGCT	1	false
+ACCAAACGTTCTCACC	NDFIP1	CTGCCATTATGG	1	false
+ACCAAACGTTCTCACC	NPTN	ATGGATTATAGG	1	false
+ACCAAACGTTCTCACC	NR3C1	GTGTTGTTAATG	1	false
+ACCAAACGTTCTCACC	ORAOV1	GAGTTCCTCGAA	1	false
+ACCAAACGTTCTCACC	PFN2	AACTACTACCTA	1	false
+ACCAAACGTTCTCACC	PGAP1	CAAGTATCCGGC	1	false
+ACCAAACGTTCTCACC	PRKAR1B	CTAAGATTGTTT	1	false
+ACCAAACGTTCTCACC	PRKDC	AGCACCTCAGCT	1	false
+ACCAAACGTTCTCACC	PSIP1	TTTATGAAACGG	1	false
+ACCAAACGTTCTCACC	PSMA1	TCCCGTTACACA	1	false
+ACCAAACGTTCTCACC	PTPN18	AAATTCTAATAC	1	false
+ACCAAACGTTCTCACC	RAP1GAP2	ATGCTCGTCCAG	1	false
+ACCAAACGTTCTCACC	RIMS1	TCTTGGTACAAA	1	false
+ACCAAACGTTCTCACC	RN7SK	TCATTGCTAATT	1	false
+ACCAAACGTTCTCACC	RPL10A	ACGAGTAACATC	1	false
+ACCAAACGTTCTCACC	RPL30	CTGGAAGCGTAA	1	false
+ACCAAACGTTCTCACC	RPL34	TGCACCACAAGG	1	false
+ACCAAACGTTCTCACC	RPLP1	AGAGCTTATCTA	1	false
+ACCAAACGTTCTCACC	RYR2	CAGCAGTCCGTA	1	false
+ACCAAACGTTCTCACC	SAMD8	TCCGCCATATTA	1	false
+ACCAAACGTTCTCACC	SDF4	TTGAGTGTAAGT	1	false
+ACCAAACGTTCTCACC	SH3PXD2A	GATTTGGGGCGT	1	false
+ACCAAACGTTCTCACC	SLC17A7	AATTGATTAAGT	1	false
+ACCAAACGTTCTCACC	SLC26A10	TAGCGTCTTTAG	1	false
+ACCAAACGTTCTCACC	SLC8A1	CCGCATTCCAGG	1	false
+ACCAAACGTTCTCACC	SLC8A1-AS1	CCTTACAGGCAA	1	false
+ACCAAACGTTCTCACC	SLF1	TAATCGTTCGGC	1	false
+ACCAAACGTTCTCACC	SMC1A	CTCATGATTGTT	1	false
+ACCAAACGTTCTCACC	SMURF1	GGCTCCATTGAC	1	false
+ACCAAACGTTCTCACC	SNRNP70	CGAACTTGCTGC	1	false
+ACCAAACGTTCTCACC	SPATA18	CATCAACATCGG	1	false
+ACCAAACGTTCTCACC	SPTBN1	TCTTATGTCTCG	1	false
+ACCAAACGTTCTCACC	SRSF11	TCCAGGCTGCAT	2	false
+ACCAAACGTTCTCACC	SSTR2	AATTGTATCTTA	1	false
+ACCAAACGTTCTCACC	STRN	TGATAGTCCCCG	1	false
+ACCAAACGTTCTCACC	SV2B	TACAAAAATGTT	1	false
+ACCAAACGTTCTCACC	SYNE1	GATTTCTAAGTC	1	false
+ACCAAACGTTCTCACC	TMED4	ACTTCGTGTTCA	1	false
+ACCAAACGTTCTCACC	TMEM117	GGTATGCGTGTA	1	false
+ACCAAACGTTCTCACC	TMEM246	GACATAGCTAAA	1	false
+ACCAAACGTTCTCACC	TMEM87A	TGCCAGCTGACT	1	false
+ACCAAACGTTCTCACC	TMOD2	AATTAAGAGTTA	1	false
+ACCAAACGTTCTCACC	TOMM7	GAATACTCTGGT	1	false
+ACCAAACGTTCTCACC	TRIM27	CCAAGTCCGGAT	1	false
+ACCAAACGTTCTCACC	TRIM44	GATCTGCCCGAC	1	false
+ACCAAACGTTCTCACC	TRIM59	TATATATGCGAT	1	false
+ACCAAACGTTCTCACC	TTC28	ATTCTAGACCCT	1	false
+ACCAAACGTTCTCACC	TTC9B	GCCTCCCTTAGT	1	false
+ACCAAACGTTCTCACC	TVP23A	TTCTCTTTTTCC	1	false
+ACCAAACGTTCTCACC	UNC119	GCCGGAGTTTGC	1	false
+ACCAAACGTTCTCACC	UQCRH	TCACTCATATGT	1	false
+ACCAAACGTTCTCACC	USMG5	ATTTAGTAAATG	2	false
+ACCAAACGTTCTCACC	USP25	AGGACCCGATCA	1	false
+ACCAAACGTTCTCACC	USP25	TGCAGTCCCCGG	1	false
+ACCAAACGTTCTCACC	UTP6	CCCAGGCAGCTA	1	false
+ACCAAACGTTCTCACC	VGLL4	CCGACGGACACA	1	false
+ACCAAACGTTCTCACC	YBEY	TTGCTGGATTTA	1	false
+ACCAAACGTTCTCACC	YEATS2	CTCAACATCATG	1	false
+ACCAAACGTTCTCACC	YWHAH	GATATTGGGTCA	1	false
+ACCAAACGTTCTCACC	ZC2HC1A	AGATGGAAATCC	1	false
+ACCAAACGTTCTCACC	ZFP28	CCTTTTACTGTA	1	false
+ACCAAACGTTCTCACC	ZFYVE16	ATGCAACTTCGG	2	false
+ACCAAACGTTCTCACC	ZNF516	GTGATTGTGCGC	1	false
+ACCAAACGTTCTCACC	ZNF528	CATCCGGACTTA	1	false
+ACCAAACGTTCTCACC	ZRANB3	CTGACTGGATTC	1	false



View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/a1aaded58271ad0f43a0f76fc67a04382ffd1992...8887ed0e7c42eded3e10cd109c76d320c8434fc8

-- 
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/a1aaded58271ad0f43a0f76fc67a04382ffd1992...8887ed0e7c42eded3e10cd109c76d320c8434fc8
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