htsjdk.variant.variantcontext.Allele.isCalled()方法的使用及代码示例

本文整理了Java中htsjdk.variant.variantcontext.Allele.isCalled()方法的一些代码示例，展示了Allele.isCalled()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Allele.isCalled()方法的具体详情如下：
包路径：htsjdk.variant.variantcontext.Allele
类名称：Allele
方法名：isCalled

Allele.isCalled介绍

暂无

代码示例

代码示例来源：origin: org.seqdoop/htsjdk

private void validateGenotypes() {
if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null");
for ( final Genotype g : this.genotypes ) {
if ( g.isAvailable() ) {
for ( Allele gAllele : g.getAlleles() ) {
if ( ! hasAllele(gAllele) && gAllele.isCalled() )
throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
}
}
}
}

代码示例来源：origin: com.github.samtools/htsjdk

/**
* helper routine for subcontext
* @param genotypes genotypes
* @return allele set
*/
private final Set allelesOfGenotypes(Collection genotypes) {
final Set alleles = new HashSet<>();
boolean addedref = false;
for ( final Genotype g : genotypes ) {
for ( final Allele a : g.getAlleles() ) {
addedref = addedref || a.isReference();
if ( a.isCalled() )
alleles.add(a);
}
}
if ( ! addedref ) alleles.add(getReference());
return alleles;
}

代码示例来源：origin: samtools/htsjdk

/**
* helper routine for subcontext
* @param genotypes genotypes
* @return allele set
*/
private final Set allelesOfGenotypes(Collection genotypes) {
final Set alleles = new HashSet<>();
boolean addedref = false;
for ( final Genotype g : genotypes ) {
for ( final Allele a : g.getAlleles() ) {
addedref = addedref || a.isReference();
if ( a.isCalled() )
alleles.add(a);
}
}
if ( ! addedref ) alleles.add(getReference());
return alleles;
}

代码示例来源：origin: org.seqdoop/htsjdk

/**
* helper routine for subcontext
* @param genotypes genotypes
* @return allele set
*/
private final Set allelesOfGenotypes(Collection genotypes) {
final Set alleles = new HashSet();
boolean addedref = false;
for ( final Genotype g : genotypes ) {
for ( final Allele a : g.getAlleles() ) {
addedref = addedref || a.isReference();
if ( a.isCalled() )
alleles.add(a);
}
}
if ( ! addedref ) alleles.add(getReference());
return alleles;
}

代码示例来源：origin: samtools/htsjdk

private void validateGenotypes() {
if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null");
for ( int i = 0; i Genotype genotype = genotypes.get(i);
if ( genotype.isAvailable() ) {
final List alleles = genotype.getAlleles();
for ( int j = 0, size = alleles.size(); j final Allele gAllele = alleles.get(j);
if ( ! hasAllele(gAllele) && gAllele.isCalled() )
throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
}
}
}
}

代码示例来源：origin: com.github.samtools/htsjdk

private void validateGenotypes() {
if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null");
for ( int i = 0; i Genotype genotype = genotypes.get(i);
if ( genotype.isAvailable() ) {
final List alleles = genotype.getAlleles();
for ( int j = 0, size = alleles.size(); j final Allele gAllele = alleles.get(j);
if ( ! hasAllele(gAllele) && gAllele.isCalled() )
throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
}
}
}
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testCreatingNoCallAlleles() {
Assert.assertTrue(NoCall.isNonReference());
Assert.assertFalse(NoCall.isReference());
Assert.assertFalse(NoCall.basesMatch(Allele.NO_CALL_STRING));
Assert.assertEquals(NoCall.length(), 0);
Assert.assertTrue(NoCall.isNoCall());
Assert.assertFalse(NoCall.isCalled());
}

代码示例来源：origin: broadgsa/gatk-protected

} else if (a.isCalled()) {
final Allele newAllele;
if (extraBaseCount > 0) {

代码示例来源：origin: broadgsa/gatk

if (allele.isCalled()) {
String alleleString = allele.toString();
alleleCounts.putIfAbsent(alleleString, 0);

代码示例来源：origin: broadgsa/gatk-protected

if (allele.isCalled()) {
hasCalledAlleles = true;
break;