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Correct doc string for IGNORED_CHROMOSOMES: default is not to ignore … #429

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Jun 20, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ public class GatherDigitalAlleleCounts extends GeneFunctionCommandLineBase {
@Argument(doc = "At least <FRACTION_SAMPLES_PASSING> samples must have genotype scores >= GQ_THRESHOLD for the variant in the VCF to be included in the analysis.")
public double FRACTION_SAMPLES_PASSING = 0.5;

@Argument(doc = "A list of chromosomes to omit from the analysis. The default is to omit the sex chromosomes.")
@Argument(doc = "A list of chromosomes to omit from the analysis.")
public List<String> IGNORED_CHROMOSOMES = null;

@Argument(doc = "Only output heterozygous SNPs for these samples. All samples must be heterozygous for the SNP to be analyzed.")
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