ContrastHaplotypeAndAssemblySequence

All Implemented Interfaces:
```
public class ContrastHaplotypeAndAssemblySequence

                    
```
Integration test to evaluate fasta file generated from GVCF files for the whole genome against assembly fasta Assembly fasta Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (W22). Read fasta file obtained from assembly (W22). Power: how many of the anchor perfectly match the assembly reference? Question: how frequently assembly and anchor region diverge? Created by mm2842 on 6/23/17.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public final static String`	`workdir`
`public final static String`	`alternativeSeqFile`
`public final static String`	`resultsfile`

Constructor Summary

Constructors
Constructor	Description

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static Map<String, String>`	`getMapFromFasta(String alternativeSeqFile)`	Load a fasta file in a map, headers are keys and sequences are values assumes a fasta file in which sequences are not breaked between lines
`static void`	`main(Array<String> args)`

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

- Constructor Detail
- Method Detail
  - getMapFromFasta
```
 static Map<String, String> getMapFromFasta(String alternativeSeqFile)
```
    Load a fasta file in a map, headers are keys and sequences are values assumes a fasta file in which sequences are not breaked between lines
  - main
```
 static void main(Array<String> args)
```