All Implemented Interfaces:


public class SmallSeqPaths

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public final static String`	`fastaSuffix`
`public final static String`	`refGenomeName`
`public final static Multimap<String, String>`	`genomeNames`
`public static TaxaList`	`taxaList`
`public final static String`	`refGenomeFile`
`public final static String`	`gvcfServerPath`
`public static String`	`smallSeqBaseDir`
`public static String`	`smallSeqBaseRemoteGvcfDir`
`public static String`	`postgresDockerDir`
`public static String`	`postgresDataDir`
`public static String`	`baseDir`
`public static String`	`baseGvcfDir`
`public static String`	`baseDirDocker`
`public static String`	`baseGVCFDirDocker`
`public static String`	`inputDir`
`public static String`	`inputDirDocker`
`public static String`	`assemblyDir`
`public static String`	`assemblyDirDocker`
`public static String`	`assemblyServerDir`
`public static String`	`loadDBDir`
`public static String`	`loadDBDirDocker`
`public static String`	`fastqDir`
`public static String`	`fastqDirDocker`
`public static String`	`bamDir`
`public static String`	`bamDirDocker`
`public static String`	`bamDedupDir`
`public static String`	`bamDedupDirDocker`
`public static String`	`bamMapQDir`
`public static String`	`bamMapQDirDocker`
`public static String`	`gvcfDir`
`public static String`	`gvcfDirDocker`
`public static String`	`localGvcfDir`
`public static String`	`localGvcfDirDocker`
`public static String`	`refGenomeDir`
`public static String`	`refGenomeDirDocker`
`public static String`	`refServerDir`
`public static String`	`outputDir`
`public static String`	`outputDirDocker`
`public static String`	`alignDir`
`public static String`	`alignDirDocker`
`public static String`	`alignGVCFDir`
`public static String`	`alignGVCFDirDocker`
`public static String`	`tempFileDir`
`public static String`	`tempFileDirDocker`
`public static String`	`answerDir`
`public static String`	`samDir`
`public static String`	`pangenomeDir`
`public static String`	`pangenomeDirDocker`
`public static String`	`genotypingFastqDir`
`public static String`	`genotypingFastqDirDocker`
`public static String`	`dataDir`
`public static String`	`dataDirDocker`
`public static String`	`pangenomePath`
`public static String`	`pangenomePathDocker`
`public static String`	`refGenomePath`
`public static String`	`refGenomePathDocker`
`public static String`	`phgDBName`
`public static String`	`phgDBNameDocker`
`public static String`	`postgresDockerfile`
`public static String`	`phgDBNamePostgres`
`public static String`	`postgresUser`
`public static String`	`postgresUserPwd`
`public static String`	`postgresHost`
`public static String`	`postgresPort`
`public static String`	`postgresImageName`
`public static String`	`postgresContainer`
`public static String`	`anchorBedFileBase`
`public static String`	`anchorBedFileBaseDocker`
`public static String`	`anchorBedFile`
`public static String`	`anchorGFFFileBase`
`public static String`	`anchorGFFFileBaseDocker`
`public static String`	`anchorGFFFile`
`public static String`	`vcfFile`
`public static String`	`vcfDummy`
`public static String`	`vcfDummyDocker`
`public static String`	`dbConfigFile`
`public static String`	`dbConfigFileDocker`
`public static String`	`dbConfigFileName`
`public static String`	`dbDockerConfigFile`
`public static String`	`dbDockerConfigFileDockerPath`
`public static String`	`dbPostgresConfigFileName`
`public static String`	`dbDockerPostgresConfigFile`
`public static String`	`dbDockerPostgresConfigFileDockerPath`
`public static String`	`asmKeyFile`
`public static String`	`asmKeyFileDocker`
`public static String`	`asmMAFKeyFile`
`public static String`	`asmMAFKeyFileDocker`
`public static String`	`keyFile`
`public static String`	`keyFileDocker`
`public static String`	`genotypingKeyFile`
`public static String`	`genotypingKeyFileDocker`
`public static String`	`genotypingPathKeyFile`
`public static String`	`genotypingPathKeyFileDocker`
`public static String`	`genotypingDebugDirDocker`
`public static String`	`genotypingDebugDir`
`public static String`	`refLoadDataFileName`
`public static String`	`refLoadDataFile`
`public static String`	`refLoadDataFileDocker`
`public static String`	`rankingFile`
`public static String`	`rankingFileDocker`
`public final static String`	`dockerImageName`

Constructor Summary

Constructors
Constructor	Description

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static void`	`resetBaseDirectory(String baseDirectory)`

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

Constructor Detail

Method Detail

resetBaseDirectory

 static void resetBaseDirectory(String baseDirectory)

Class SmallSeqPaths

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Method Detail

resetBaseDirectory