Projects >> gatk >>4d88e7295890d3c183b77f8dfcd411937425f49f

Chunk
Conflicting content 
    @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
    private boolean KEEP_ORIGINAL_CHR_COUNTS = false;

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    @Input(fullName="discordance", shortName =  "disc", doc="Output variants that were not called on a ROD comparison track", required=false)
    private RodBinding discordanceTrack = RodBinding.makeUnbound(VariantContext.class);

    @Input(fullName="concordance", shortName =  "conc", doc="Output variants that were also called on a ROD comparison track", required=false)
    private RodBinding concordanceTrack = RodBinding.makeUnbound(VariantContext.class);

>>>>>>> f049461120b0f333964011a5e1ad20cc93f61992
    @Hidden
    @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
    private boolean KEEP_AF_SPECTRUM = false;
Solution content 
    @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
    private boolean KEEP_ORIGINAL_CHR_COUNTS = false;

    @Argument(fullName="discordance", shortName =  "disc", doc="Output variants that were not called on a ROD comparison track", required=false)
    private RodBinding discordanceTrack = RodBinding.makeUnbound(VariantContext.class);

    @Argument(fullName="concordance", shortName =  "conc", doc="Output variants that were also called on a ROD comparison track", required=false)
    private RodBinding concordanceTrack = RodBinding.makeUnbound(VariantContext.class);

    @Hidden
    @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
    private boolean KEEP_AF_SPECTRUM = false;
File
SelectVariants.java
Developer's decision
Manual
Kind of conflict
Annotation
Attribute
Method invocation
Chunk
Conflicting content 
    public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";

    public static final String dbsnpDataLocation = GATKDataLocation;
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    public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
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    public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf";
    public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
>>>>>>> f049461120b0f333964011a5e1ad20cc93f61992
    public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";

    public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
Solution content 
    public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";

    public static final String dbsnpDataLocation = GATKDataLocation;
    public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf";
    public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";

    public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
File
BaseTest.java
Developer's decision
Combination
Kind of conflict
Attribute