net.maizegenetics.pangenome.pipelineTests

Class ContrastHaplotypeAndAssemblySequence

java.lang.Object

net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence

public class ContrastHaplotypeAndAssemblySequence
extends Object

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.

Field Summary

Fields

Modifier and Type	Field and Description
static String	alternativeSeqFile
static String	resultsfile
static String	workdir

Constructor Summary

Constructors

Constructor and Description
ContrastHaplotypeAndAssemblySequence()

Method Summary

Modifier and Type	Method and 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(String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

workdir

public static final String workdir

See Also:

Constant Field Values

alternativeSeqFile

public static final String alternativeSeqFile

See Also:

Constant Field Values

resultsfile

public static final String resultsfile

See Also:

Constant Field Values

Constructor Detail

ContrastHaplotypeAndAssemblySequence

public ContrastHaplotypeAndAssemblySequence()

Method Detail

getMapFromFasta

public static Map<String,String> getMapFromFasta(String alternativeSeqFile)
                                          throws IOException

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

Throws:

IOException

main

public static void main(String[] args)