Serialized Form

Package gorsat.commands

Class gorsat.commands.Pyspark

class Pyspark extends gorsat.Commands.CommandInfo implements Serializable

Package gorsat.process

Class gorsat.process.FilterParams

class FilterParams extends Object implements Serializable

Serialized Fields

colType

String[] colType

headersplit

String[] headersplit

paramString

String paramString

Class gorsat.process.GorMapFunction

class GorMapFunction extends Object implements Serializable

Serialized Fields

calcType

String calcType

func

scala.Function1 func

replaceIndex

int replaceIndex

Class gorsat.process.GorSpark

class GorSpark extends Object implements Serializable

Serialized Fields

gorcmd

String gorcmd

gorroot

String gorroot

header

String header

jobId

String jobId

nor

boolean nor

schema

org.apache.spark.sql.types.StructType schema

uri

String uri

Class gorsat.process.GorSparkExternalFunction

class GorSparkExternalFunction extends Object implements Serializable

Serialized Fields

cmd

String cmd

fetchHeader

boolean fetchHeader

goroot

String goroot

header

String header

schema

org.apache.spark.sql.types.StructType schema

Class gorsat.process.GorSparkMaterialize

class GorSparkMaterialize extends GorSpark implements Serializable

Serialized Fields

max

int max

Class gorsat.process.NorMapFunction

class NorMapFunction extends GorMapFunction implements Serializable

Class gorsat.process.PNFilterFunction

class PNFilterFunction extends Object implements Serializable

Serialized Fields

colnum

int colnum

pns

Set<String> pns

Class gorsat.process.ProcessIteratorAdaptor

class ProcessIteratorAdaptor extends org.gorpipe.gor.model.GenomicIteratorBase implements Serializable

Serialized Fields

allowerror

boolean allowerror

breader

BufferedReader breader

errorStr

StringBuilder errorStr

is

InputStream is

line

String line

mustReCheck

boolean mustReCheck

myHasNext

boolean myHasNext

nor

boolean nor

outThread

gorsat.process.ProcessIteratorAdaptor.OutThread outThread

proc

Process proc

processName

String processName

rowSource

Iterator<org.gorpipe.gor.model.Row> rowSource

skipheader

boolean skipheader

Class gorsat.process.SourceProvider

class SourceProvider extends Object implements Serializable

Serialized Fields

context

org.gorpipe.gor.session.GorContext context

dynSource

gorsat.DynIterator.DynamicRowSource dynSource

executeNor

boolean executeNor

header

String header

inputSource

String inputSource

isNor

boolean isNor

iteratorCommand

String iteratorCommand

source

org.gorpipe.gor.model.GenomicIterator source

usedFiles

String[] usedFiles

Class gorsat.process.SourceProvider$

class SourceProvider$ extends Object implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Package gorsat.spark

Class gorsat.spark.GordFunction

class GordFunction extends Object implements Serializable

Serialized Fields

encoder

org.apache.spark.sql.catalyst.encoders.ExpressionEncoder<org.apache.spark.sql.Row> encoder

header

String header

serializer

org.apache.spark.sql.catalyst.encoders.ExpressionEncoder.Serializer<org.apache.spark.sql.Row> serializer

Class gorsat.spark.GorFileFormat

class GorFileFormat extends org.apache.spark.sql.execution.datasources.csv.CSVFileFormat implements Serializable

Class gorsat.spark.GorReaderFactory

class GorReaderFactory extends Object implements Serializable

Serialized Fields

aliasFile

String aliasFile

cacheDir

String cacheDir

cacheFile

String cacheFile

configFile

String configFile

jobId

String jobId

projectRoot

String projectRoot

redisUri

String redisUri

schema

org.apache.spark.sql.types.StructType schema

securityContext

String securityContext

streamKey

String streamKey

useCpp

String useCpp

Class gorsat.spark.GorSpecificInputPartition

class GorSpecificInputPartition extends Object implements Serializable

Serialized Fields

i

int[] i

j

int[] j

Class gorsat.spark.GorSpecificReaderFactory

class GorSpecificReaderFactory extends Object implements Serializable

Package org.gorpipe.spark

Class org.gorpipe.spark.GorFilterFunction

class GorFilterFunction extends org.gorpipe.gor.function.GorRowFilterFunction<org.gorpipe.gor.model.Row> implements Serializable

Class org.gorpipe.spark.GorHeaderInferFunction

class GorHeaderInferFunction extends Object implements Serializable

Serialized Fields

convMap

Map<String,Character> convMap

Class org.gorpipe.spark.GorPartition

class GorPartition extends Object implements Serializable

Serialized Fields

p

int p

Class org.gorpipe.spark.GorPipeFunction

class GorPipeFunction extends Object implements Serializable

Serialized Fields

cmd

String cmd

header

String header

Class org.gorpipe.spark.GorpipeRDD

class GorpipeRDD extends org.apache.spark.rdd.RDD<T extends Object> implements Serializable

Serialized Fields

evidence$5

scala.reflect.ClassTag<T extends Object> evidence$5

gor

boolean gor

header

String header

org$gorpipe$spark$GorpipeRDD$$encoder

org.apache.spark.sql.catalyst.encoders.ExpressionEncoder<T extends Object> org$gorpipe$spark$GorpipeRDD$$encoder

pipeStep

gorsat.Commands.Analysis pipeStep

Class org.gorpipe.spark.GorpWriter

class GorpWriter extends Object implements Serializable

Serialized Fields

path

String path

Class org.gorpipe.spark.GorQueryRDD

class GorQueryRDD extends org.apache.spark.rdd.RDD<String> implements Serializable

Serialized Fields

aliasFile

String aliasFile

allowFail

Boolean[] allowFail

cacheDirectory

String cacheDirectory

cacheFiles

String[] cacheFiles

commandSignatures

String[] commandSignatures

commandsToExecute

String[] commandsToExecute

configFile

String configFile

jobIds

String[] jobIds

projectDirectory

String projectDirectory

redisKey

String redisKey

redisUri

String redisUri

secCtxs

String[] secCtxs

Class org.gorpipe.spark.GorRDD

class GorRDD extends org.apache.spark.rdd.RDD<org.gorpipe.gor.model.Row> implements Serializable

Serialized Fields

evidence$6

scala.reflect.ClassTag<T extends Object> evidence$6

gor

boolean gor

gorcmd

String gorcmd

header

String header

Class org.gorpipe.spark.GorSparkArrayInferFunction

class GorSparkArrayInferFunction extends Object implements Serializable

Class org.gorpipe.spark.GorSparkRow

class GorSparkRow extends SparkRow implements Serializable

Class org.gorpipe.spark.GorSparkRowBase

class GorSparkRowBase extends org.gorpipe.gor.model.Row implements Serializable

Class org.gorpipe.spark.GorSparkRowFilterFunction

class GorSparkRowFilterFunction extends org.gorpipe.gor.function.GorRowFilterFunction<org.gorpipe.gor.model.Row> implements Serializable

Class org.gorpipe.spark.GorSparkRowInferFunction

class GorSparkRowInferFunction extends org.gorpipe.gor.function.GorRowInferFunction implements Serializable

Class org.gorpipe.spark.GorSparkRowMapFunction

class GorSparkRowMapFunction extends org.gorpipe.gor.function.GorRowMapFunction implements Serializable

Serialized Fields

schema

org.apache.spark.sql.types.StructType schema

Class org.gorpipe.spark.GorSparkRowQueryFunction

class GorSparkRowQueryFunction extends org.gorpipe.gor.function.GorRowQueryFunction implements Serializable

Class org.gorpipe.spark.Gorz

class Gorz extends Object implements Serializable

Serialized Fields

block

String block

CHROM

String CHROM

POS

int POS

Class org.gorpipe.spark.Gorz$

class Gorz$ extends scala.runtime.AbstractFunction3<String,Object,String,org.gorpipe.spark.Gorz> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.GorzFlatMap

class GorzFlatMap extends Object implements Serializable

Serialized Fields

buffer

byte[] buffer

Class org.gorpipe.spark.GorzIterator

class GorzIterator extends Object implements Serializable

Serialized Fields

header

String header

Class org.gorpipe.spark.GorzStr

class GorzStr extends Object implements Serializable

Serialized Fields

block

String block

CHROM

String CHROM

POS

String POS

Class org.gorpipe.spark.GorzStr$

class GorzStr$ extends scala.runtime.AbstractFunction3<String,String,String,org.gorpipe.spark.GorzStr> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.HeaderFunction

class HeaderFunction extends Object implements Serializable

Serialized Fields

cmd

String cmd

header

String header

Class org.gorpipe.spark.HeaderInferFunction

class HeaderInferFunction extends Object implements Serializable

Serialized Fields

cmd

String cmd

header

String header

Class org.gorpipe.spark.LongGorSparkRow

class LongGorSparkRow extends GorSparkRow implements Serializable

Class org.gorpipe.spark.NorFilterFunction

class NorFilterFunction extends org.gorpipe.gor.function.GorRowFilterFunction<org.gorpipe.gor.model.Row> implements Serializable

Class org.gorpipe.spark.NorSparkRow

class NorSparkRow extends SparkRow implements Serializable

Class org.gorpipe.spark.NorSparkRowFilterFunction

class NorSparkRowFilterFunction extends GorFilterFunction implements Serializable

Class org.gorpipe.spark.PgorRDD

class PgorRDD extends org.apache.spark.rdd.RDD<org.gorpipe.gor.model.Row> implements Serializable

Serialized Fields

filter

String filter

gorcmd

String gorcmd

Class org.gorpipe.spark.PipeFunction

class PipeFunction extends Object implements Serializable

Serialized Fields

cmd

String cmd

header

String header

Class org.gorpipe.spark.QueryRDD

class QueryRDD extends org.apache.spark.rdd.RDD<String> implements Serializable

Serialized Fields

cacheDir

String cacheDir

commandSignatures

String[] commandSignatures

commandsToExecute

String[] commandsToExecute

hash

String hash

header

boolean header

projectDirectory

String projectDirectory

sparkSession

org.apache.spark.sql.SparkSession sparkSession

sqlContext

org.apache.spark.sql.SQLContext sqlContext

Class org.gorpipe.spark.Result

class Result extends Object implements Serializable

Serialized Fields

ALT

String ALT

CHROM

String CHROM

ID

String ID

M

String M

POS

int POS

REF

String REF

Class org.gorpipe.spark.Result$

class Result$ extends scala.runtime.AbstractFunction6<String,Object,String,String,String,String,org.gorpipe.spark.Result> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.RowGorRDD

class RowGorRDD extends org.gorpipe.spark.PgorRDD<org.gorpipe.gor.model.Row> implements Serializable

Class org.gorpipe.spark.SparkGOR.Dbsnp

class Dbsnp extends Object implements Serializable

Serialized Fields

ALT

String ALT

CHROM

String CHROM

ID

String ID

POS

int POS

REF

String REF

Class org.gorpipe.spark.SparkGOR.Dbsnp$

class Dbsnp$ extends scala.runtime.AbstractFunction5<String,Object,String,String,String,org.gorpipe.spark.SparkGOR.Dbsnp> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.SparkGOR.Gene

class Gene extends Object implements Serializable

Serialized Fields

chr

String chr

end

int end

Gene_Symbol

String Gene_Symbol

pos

int pos

Class org.gorpipe.spark.SparkGOR.Gene$

class Gene$ extends scala.runtime.AbstractFunction4<String,Object,Object,String,org.gorpipe.spark.SparkGOR.Gene> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.SparkGOR.Skat

class Skat extends Object implements Serializable

Serialized Fields

chrom

String chrom

numMarkers

int numMarkers

pvalue

String pvalue

start

int start

stop

int stop

tag

String tag

Class org.gorpipe.spark.SparkGOR.Skat$

class Skat$ extends scala.runtime.AbstractFunction6<String,Object,Object,String,Object,String,org.gorpipe.spark.SparkGOR.Skat> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.SparkGOR.Variants

class Variants extends Object implements Serializable

Serialized Fields

alt

String alt

cc

int cc

chrom

String chrom

cr

double cr

depth

int depth

filter

String filter

formatZip

String formatZip

fs

double fs

gl

int gl

pn

String pn

pos

int pos

ref

String ref

Class org.gorpipe.spark.SparkGOR.Variants$

class Variants$ extends scala.runtime.AbstractFunction12<String,Object,String,String,Object,Object,Object,Object,String,Object,String,String,org.gorpipe.spark.SparkGOR.Variants> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.SparkGorMonitor

class SparkGorMonitor extends org.gorpipe.gor.monitor.GorMonitor implements Serializable

Serialized Fields

jobId

String jobId

Class org.gorpipe.spark.SparkGorMonitorFactory

class SparkGorMonitorFactory extends Object implements Serializable

Class org.gorpipe.spark.SparkGorRow

class SparkGorRow extends GorSparkRowBase implements Serializable

Serialized Fields

row

org.gorpipe.gor.model.Row row

schema

org.apache.spark.sql.types.StructType schema

Class org.gorpipe.spark.sparkGorTest.Person

class Person extends Object implements Serializable

Serialized Fields

age

long age

name

String name

Class org.gorpipe.spark.sparkGorTest.Person$

class Person$ extends scala.runtime.AbstractFunction2<String,Object,org.gorpipe.spark.sparkGorTest.Person> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class org.gorpipe.spark.SparkRow

class SparkRow extends GorSparkRowBase implements Serializable

Serialized Fields

row

org.apache.spark.sql.Row row

Class org.gorpipe.spark.TestGorRDD

class TestGorRDD extends org.apache.spark.rdd.RDD<org.gorpipe.gor.model.Row> implements Serializable

Serialized Fields

gor

boolean gor

gorcmd

String gorcmd

header

String header

Package org.gorpipe.spark.udfs

Class org.gorpipe.spark.udfs.ArrayToVector

class ArrayToVector extends Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArray

class CharToDoubleArray extends Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArrayMissing

class CharToDoubleArrayMissing extends Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArrayMissingParallel

class CharToDoubleArrayMissingParallel extends Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArrayParallel

class CharToDoubleArrayParallel extends Object implements Serializable

Class org.gorpipe.spark.udfs.CommaToDoubleArray

class CommaToDoubleArray extends Object implements Serializable

Class org.gorpipe.spark.udfs.CommaToDoubleMatrix

class CommaToDoubleMatrix extends Object implements Serializable

Class org.gorpipe.spark.udfs.CommaToIntArray

class CommaToIntArray extends Object implements Serializable

Class org.gorpipe.spark.udfs.ListToVector

class ListToVector extends Object implements Serializable

Class org.gorpipe.spark.udfs.VectorToArray

class VectorToArray extends Object implements Serializable