MergeGVCFUtils

All Implemented Interfaces:
```
@Deprecated() 
public class MergeGVCFUtils

                    
```
Created by zrm22 on 11/7/17. This class borrows code from GATK. Eventually we should just bring in the GATK jar and use the method directly. Some of this will need to be cleaned up as it uses a lot of extra methods. I just copied them till the class will compile. TODO Clean up this class as it is thrown together to make it work.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static GenotypeTable`	`createGenotypeTableFromHaplotypeNodes(ReferenceRange refRange, List<HaplotypeNode> nodesWithVariantContexts, GenomeSequence referenceSequence)`	Method to make a genotypeTable from a list of Haplotype Nodes.
`static String`	`removeHaplotypeCaller(String taxonName)`	Simple method to remove the _Haplotype_Caller from the taxon name
`static GenotypeTable`	`createGenotypeTableFromGVCFs(ReferenceRange refRange, Multimap<Taxon, VariantContext> taxonToVariantListMap, GenomeSequence referenceSequence)`	This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable
`static boolean`	`isRefBlock(VariantContext vc)`	Simple method to check to see if the Variant is a reference block
`static GenotypeTable`	`removeIndels(GenotypeTable baseAlign)`	Method to Remove indels from the GenotypeTable.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
- Method Detail
  - createGenotypeTableFromHaplotypeNodes
```
 static GenotypeTable createGenotypeTableFromHaplotypeNodes(ReferenceRange refRange, List<HaplotypeNode> nodesWithVariantContexts, GenomeSequence referenceSequence)
```
    Method to make a genotypeTable from a list of Haplotype Nodes. This method will simply make the GenotypeTable encoding indels as either + or - depending on what is actually stored in the HaplotypeNode In other steps, the indels will be filtered out and then will be added back in when consensus is made.
  - removeHaplotypeCaller
```
 static String removeHaplotypeCaller(String taxonName)
```
    Simple method to remove the _Haplotype_Caller from the taxon name
  - createGenotypeTableFromGVCFs
```
 static GenotypeTable createGenotypeTableFromGVCFs(ReferenceRange refRange, Multimap<Taxon, VariantContext> taxonToVariantListMap, GenomeSequence referenceSequence)
```
    This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable
  - isRefBlock
```
 static boolean isRefBlock(VariantContext vc)
```
    Simple method to check to see if the Variant is a reference block
  - removeIndels
```
 static GenotypeTable removeIndels(GenotypeTable baseAlign)
```
    Method to Remove indels from the GenotypeTable. Basically if it has a + or - in any of the calls, we filter out.