本文整理汇总了Java中htsjdk.variant.variantcontext.Genotype.getExtendedAttributes方法的典型用法代码示例。如果您正苦于以下问题：Java Genotype.getExtendedAttributes方法的具体用法？Java Genotype.getExtendedAttributes怎么用？Java Genotype.getExtendedAttributes使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.variant.variantcontext.Genotype的用法示例。
在下文中一共展示了Genotype.getExtendedAttributes方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: cleanupGenotypeAnnotations
import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
/**
* Cleans up genotype-level annotations that need to be updated.
* 1. move MIN_DP to DP if present
* 2. propagate DP to AD if not present
* 3. remove SB if present
* 4. change the PGT value from "0|1" to "1|1" for homozygous variant genotypes
*
* @param VC the VariantContext with the Genotypes to fix
* @param createRefGTs if true we will also create proper hom ref genotypes since we assume the site is monomorphic
* @return a new set of Genotypes
*/
private List<Genotype> cleanupGenotypeAnnotations(final VariantContext VC, final boolean createRefGTs) {
final GenotypesContext oldGTs = VC.getGenotypes();
final List<Genotype> recoveredGs = new ArrayList<>(oldGTs.size());
for ( final Genotype oldGT : oldGTs ) {
final Map<String, Object> attrs = new HashMap<>(oldGT.getExtendedAttributes());
final GenotypeBuilder builder = new GenotypeBuilder(oldGT);
int depth = oldGT.hasDP() ? oldGT.getDP() : 0;
// move the MIN_DP to DP
if ( oldGT.hasExtendedAttribute("MIN_DP") ) {
depth = Integer.parseInt((String)oldGT.getAnyAttribute("MIN_DP"));
builder.DP(depth);
attrs.remove("MIN_DP");
}
// remove SB
attrs.remove("SB");
// update PGT for hom vars
if ( oldGT.isHomVar() && oldGT.hasExtendedAttribute(HaplotypeCaller.HAPLOTYPE_CALLER_PHASING_GT_KEY) ) {
attrs.put(HaplotypeCaller.HAPLOTYPE_CALLER_PHASING_GT_KEY, "1|1");
}
// create AD if it's not there
if ( !oldGT.hasAD() && VC.isVariant() ) {
final int[] AD = new int[VC.getNAlleles()];
AD[0] = depth;
builder.AD(AD);
}
if ( createRefGTs ) {
final int ploidy = oldGT.getPloidy();
final List<Allele> refAlleles = Collections.nCopies(ploidy,VC.getReference());
//keep 0 depth samples as no-call
if (depth > 0) {
builder.alleles(refAlleles);
}
// also, the PLs are technically no longer usable
builder.noPL();
}
recoveredGs.add(builder.noAttributes().attributes(attrs).make());
}
return recoveredGs;
}
示例2: cleanupGenotypeAnnotations
import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
private List<Genotype> cleanupGenotypeAnnotations(final VariantContext VC, final boolean createRefGTs) {
final GenotypesContext oldGTs = VC.getGenotypes();
final List<Genotype> recoveredGs = new ArrayList<>(oldGTs.size());
for (final Genotype oldGT : oldGTs) {
final Map<String, Object> attrs = new HashMap<>(oldGT.getExtendedAttributes());
final GenotypeBuilder builder = new GenotypeBuilder(oldGT);
int depth = oldGT.hasDP() ? oldGT.getDP() : 0;
// move the MIN_DP to DP
if (oldGT.hasExtendedAttribute(GaeaVCFConstants.MIN_DP_FORMAT_KEY)) {
depth = Integer.parseInt((String) oldGT.getAnyAttribute(GaeaVCFConstants.MIN_DP_FORMAT_KEY));
builder.DP(depth);
attrs.remove(GaeaVCFConstants.MIN_DP_FORMAT_KEY);
}
// move the GQ to RGQ
if (createRefGTs && oldGT.hasGQ()) {
builder.noGQ();
attrs.put(GaeaVCFConstants.REFERENCE_GENOTYPE_QUALITY, oldGT.getGQ());
}
// remove SB
attrs.remove(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY);
// update PGT for hom vars
if (oldGT.isHomVar() && oldGT.hasExtendedAttribute(GaeaVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY)) {
attrs.put(GaeaVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY, "1|1");
}
// create AD if it's not there
if (!oldGT.hasAD() && VC.isVariant()) {
final int[] AD = new int[VC.getNAlleles()];
AD[0] = depth;
builder.AD(AD);
}
if (createRefGTs) {
final int ploidy = oldGT.getPloidy();
final List<Allele> refAlleles = Collections.nCopies(ploidy, VC.getReference());
// keep 0 depth samples and 0 GQ samples as no-call
if (depth > 0 && oldGT.hasGQ() && oldGT.getGQ() > 0) {
builder.alleles(refAlleles);
}
// also, the PLs are technically no longer usable
builder.noPL();
}
recoveredGs.add(builder.noAttributes().attributes(attrs).make());
}
return recoveredGs;
}