net.maizegenetics.pangenome.pipelineTests

Class EvaluateGVCFbyKnownSNPTest2

java.lang.Object

net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2

public class EvaluateGVCFbyKnownSNPTest2
extends Object

Create unit test to evaluate GVCF SNPs by comparing to known SNPs. Read a GVCF file from practical haplotype pipeline. Read in known SNP file (VCF). Identify taxa from VCF that corresponds to GVCF taxa. Loop through SNPs from GVCF and compare PHG SNPs to known SNPs. Power: how many of the known SNPs are called in PHG? Type I error: how frequently does PHG differ from known SNPs?

Note: W22-B73 IBD Chr 8: 122-147Mb Created by edbuckler on 6/22/17.

Constructor Summary

Constructors

Constructor and Description
EvaluateGVCFbyKnownSNPTest2()

Method Summary

Modifier and Type	Method and Description
void	setUp()
static void	setUpClass()
void	tearDown()
static void	tearDownClass()
void	testPHGvsKnownSNPs()
void	testSimpleGVCFReader() Test of writeToHapmap method, of class ExportUtils.

Methods inherited from class java.lang.Object

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

Constructor Detail

EvaluateGVCFbyKnownSNPTest2

public EvaluateGVCFbyKnownSNPTest2()

Method Detail

setUpClass

public static void setUpClass()
                       throws Exception

Throws:

Exception

tearDownClass

public static void tearDownClass()

setUp

public void setUp()

tearDown

public void tearDown()

testSimpleGVCFReader

public void testSimpleGVCFReader()
                          throws IOException

Test of writeToHapmap method, of class ExportUtils.

Throws:

IOException

testPHGvsKnownSNPs

public void testPHGvsKnownSNPs()