net.maizegenetics.pangenome.pipelineTests

Class EvaluateHaplotypeFastaInKnownIBDRegions

java.lang.Object

net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions

public class EvaluateHaplotypeFastaInKnownIBDRegions
extends Object

Unit test to evaluate fasta file generated from GVCF files for anchors in IBD regions to B73 Get all the anchorIDs in the IBD region of chromosome 10 Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (alternative). Power: how many of the anchor-fragments that are in IBD perfectly match the B73 ref? Question: how frequently PHG call variants in regions that should be identical? Created by mm2842 on 6/22/17.

Field Summary

Fields

Modifier and Type	Field and Description
static String	anchorIDFile
static String	fastaAlternatives
static String	resultsfile
static String	workdir

Constructor Summary

Constructors

Constructor and Description
EvaluateHaplotypeFastaInKnownIBDRegions()

Method Summary

Modifier and Type	Method and Description
static Map<String,String>	getMapFromFasta(String IBDsequences)
static Optional<Boolean>	isAltSeqSameAsRefExcludingNs(String referenceSeq, String alternativeSeq)
static void	main(String[] args)
static List<String>	readAnchorIds() Reads in list of anchor region numbers that are IBD

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

anchorIDFile

public static final String anchorIDFile

See Also:

Constant Field Values

fastaAlternatives

public static final String fastaAlternatives

See Also:

Constant Field Values

resultsfile

public static final String resultsfile

See Also:

Constant Field Values

Constructor Detail

EvaluateHaplotypeFastaInKnownIBDRegions

public EvaluateHaplotypeFastaInKnownIBDRegions()

Method Detail

readAnchorIds

public static List<String> readAnchorIds()
                                  throws IOException

Reads in list of anchor region numbers that are IBD

Throws:

IOException

isAltSeqSameAsRefExcludingNs

public static Optional<Boolean> isAltSeqSameAsRefExcludingNs(String referenceSeq,
                                                             String alternativeSeq)

getMapFromFasta

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

Throws:

IOException

main

public static void main(String[] args)