Java Code Examples for htsjdk.variant.vcf.VCFCodec#setVCFHeader()

The following examples show how to use htsjdk.variant.vcf.VCFCodec#setVCFHeader() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: VariantContextCollectionTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec() {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}
Example 2
Source File: SomaticVariantFactoryTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec() {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}
Example 3
Source File: VariantContextFromString.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec(@NotNull String sample) {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(sample));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}
Example 4
Source File: StructuralVariantFactoryTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec() {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}
Example 5
Source File: StrelkaAllelicDepthTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec() {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Lists.newArrayList(NORMAL, TUMOR));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}
Example 6
Source File: RecoveredVariantFactoryTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec() {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}
Example 7
Source File: SageHotspotAnnotationTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static VCFCodec createTestCodec() {
    VCFCodec codec = new VCFCodec();
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE));
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    return codec;
}