How to use
getOriginalAlleles
method
in
org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter

Best Java code snippets using org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter.getOriginalAlleles (Showing top 1 results out of 315)

Add the Codota plugin to your IDE and get smart completions

private void myMethod () {
 Gson g =new Gson()
GsonBuilder gsonBuilder;gsonBuilder.create()
new GsonBuilder().create()
Smart code suggestions by Codota
}

List<String> originalAlleles = getOriginalAlleles(ori);
List<String> allelesArray;
if (originalAlleles != null) {

Javadoc

Assumes that ori is in the form "POS:REF:ALT_0(,ALT_N)*:ALT_IDX". ALT_N is the n-th allele if this is the n-th variant resultant of a multiallelic vcf row

Popular methods of VariantVcfDataWriter

<init>
adjustedVariantStart
Adjust start/end if a reference base is required due to an empty allele. All variants are checked du
buildAlleles
addAnnotationInfo
addAnnotations
addCohortInfo
addStats
buildAllele
close
convertVariantToVariantContext
Convert org.opencb.biodata.models.variant.Variant into a htsjdk.variant.variantcontext.VariantContex
getOri
getOriginalAlleleIndex

Popular in Java

Start an intent from android
putExtra (Intent)
setScale (BigDecimal)
Returns a BigDecimal whose scale is the specified value, and whose value is numerically equal to thi
addToBackStack (FragmentTransaction)
FileReader (java.io)
A specialized Reader that reads from a file in the file system. All read requests made by calling me
Thread (java.lang)
A thread is a thread of execution in a program. The Java Virtual Machine allows an application to ha
Scanner (java.util)
A parser that parses a text string of primitive types and strings with the help of regular expressio
TreeMap (java.util)
A Red-Black tree based NavigableMap implementation. The map is sorted according to the Comparable of
UUID (java.util)
UUID is an immutable representation of a 128-bit universally unique identifier (UUID). There are mul
AtomicInteger (java.util.concurrent.atomic)
An int value that may be updated atomically. See the java.util.concurrent.atomic package specificati

How to use getOriginalAllelesmethodin org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter

Best Java code snippets using org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter.getOriginalAlleles (Showing top 1 results out of 315)

How to use
getOriginalAlleles
method
in
org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter