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Define GENE string constant #426

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Jun 5, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,8 @@
public class DigitalExpression extends DGECommandLineBase {

private static final Log log = Log.getInstance(DigitalExpression.class);

public static final String GENE_COLUMN = "GENE";

@Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM or BAM file to analyze.")
public File INPUT;

Expand Down Expand Up @@ -370,7 +371,7 @@ private void writeStats (final String gene, final Map<String, Integer> countMap,

private void writeHeader(final PrintStream out, final List<String> cellBarcodes) {
List<String> header = new ArrayList<>(cellBarcodes.size()+1);
header.add("GENE");
header.add(GENE_COLUMN);
header.addAll(cellBarcodes);
String h = StringUtils.join(header, "\t");
out.println(h);
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