Constant Field Values

Contents

• net.maizegenetics.*

net.maizegenetics.*

net.maizegenetics.pangenome.api.CreateGraphUtils

Modifier and Type	Constant Field	Value
public static final String	INNER_ANCHOR_METHOD	"v4_gffGenes_plus1000_trimmed"
public static final String	NO_CONSENSUS_METHOD	"Haplotype_caller"

net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference

Modifier and Type	Constant Field	Value
public static final String	anchorSummaryFile	"/Users/edbuckler/temp/assemDistRef_170621b.txt"
public static final String	localDirectory	"/Users/edbuckler/temp/chr10fastafiles/"
public static final String	loggingFile	"/Users/edbuckler/temp/logging.txt"

net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta

Modifier and Type	Constant Field	Value
public static final String	anchorSummaryFile	"/Users/edbuckler/temp/consensusSummaryMAF02_170621_all.txt"
public static final String	localConsensusDirectoryOut	"/Users/edbuckler/temp/consensus/"
public static final String	localDirectory	"/Users/edbuckler/temp/chr10fastafilesFilt/"
public static final String	loggingFile	"/Users/edbuckler/temp/logging.txt"

net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments

Modifier and Type	Constant Field	Value
public static final String	anchorSummaryFile	"/Users/edbuckler/temp/anchorSummary170620a.txt"
public static final String	localDirectory	"/Users/edbuckler/temp/chr10fastafiles/"
public static final String	localDirectoryOut	"/Users/edbuckler/temp/chr10fastafilesFilt/"
public static final String	loggingFile	"/Users/edbuckler/temp/logging.txt"

net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes

Modifier and Type	Constant Field	Value
public static final String	alignmentFiltered	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/Chrom10CleanMSA/"
public static final String	alignmentRaw	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/Chrom10raw/"
public static final String	anchorIDFile	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/test.txt"
public static final String	consensusHaplotypes	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/Chrom10CleanMSAConsensus/"
public static final String	reportFile	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/temp/report.tsv"
public static final String	workdir	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/"

net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence

Modifier and Type	Constant Field	Value
public static final String	alternativeSeqFile	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/chrom8_anchors_W22.fasta"
public static final String	resultsfile	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/Results_anchorID_W22_W22_assembly_chrom8.txt"
public static final String	workdir	"/Users/mm2842/Documents/Regulatory_Regions_Project/PHG_Hackhaton/"

net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions

Modifier and Type	Constant Field	Value
public static final String	anchorIDFile	"/Users/edbuckler/Box Sync/Hackhaton_files_June_2017/W22_unit_test_files/onehundred_IBD.txt"
public static final String	fastaAlternatives	"/Users/edbuckler/Box Sync/Hackhaton_files_June_2017/W22_unit_test_files/chrom10_anchors_W22.fasta"
public static final String	resultsfile	"/Users/edbuckler/Box Sync/Hackhaton_files_June_2017/W22_unit_test_files/Results_anchorID_IBD_W22_B73a.txt"
public static final String	workdir	"/Users/edbuckler/Box Sync/Hackhaton_files_June_2017/W22_unit_test_files/"