Serialized Form

Package gorsat.commands

Class gorsat.commands.Pyspark extends gorsat.Commands.CommandInfo implements Serializable

Package gorsat.process

Class gorsat.process.FilterParams extends java.lang.Object implements Serializable

Serialized Fields

colType

java.lang.String[] colType

headersplit

java.lang.String[] headersplit

paramString

java.lang.String paramString

Class gorsat.process.GorMapFunction extends java.lang.Object implements Serializable

Serialized Fields

calcType

java.lang.String calcType

func

scala.Function1 func

replaceIndex

int replaceIndex

Class gorsat.process.GorSpark extends java.lang.Object implements Serializable

Serialized Fields

gorcmd

java.lang.String gorcmd

gorroot

java.lang.String gorroot

header

java.lang.String header

jobId

java.lang.String jobId

nor

boolean nor

schema

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

uri

java.lang.String uri

Class gorsat.process.GorSparkExternalFunction extends java.lang.Object implements Serializable

Serialized Fields

cmd

java.lang.String cmd

fetchHeader

boolean fetchHeader

goroot

java.lang.String goroot

header

java.lang.String header

schema

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

Class gorsat.process.GorSparkMaterialize extends GorSpark implements Serializable

Serialized Fields

max

int max

Class gorsat.process.NorMapFunction extends GorMapFunction implements Serializable

Class gorsat.process.PNFilterFunction extends java.lang.Object implements Serializable

Serialized Fields

colnum

int colnum

pns

java.util.Set<java.lang.String> pns

Class gorsat.process.ProcessIteratorAdaptor extends org.gorpipe.gor.model.GenomicIteratorBase implements Serializable

Serialized Fields

allowerror

boolean allowerror

breader

java.io.BufferedReader breader

errorStr

java.lang.StringBuilder errorStr

is

java.io.InputStream is

line

java.lang.String line

mustReCheck

boolean mustReCheck

myHasNext

boolean myHasNext

nor

boolean nor

outThread

gorsat.process.ProcessIteratorAdaptor.OutThread outThread

proc

java.lang.Process proc

processName

java.lang.String processName

rowSource

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

skipheader

boolean skipheader

Class gorsat.process.SourceProvider extends java.lang.Object implements Serializable

Serialized Fields

context

org.gorpipe.gor.session.GorContext context

dynSource

gorsat.DynIterator.DynamicRowSource dynSource

executeNor

boolean executeNor

header

java.lang.String header

inputSource

java.lang.String inputSource

isNor

boolean isNor

iteratorCommand

java.lang.String iteratorCommand

source

org.gorpipe.gor.model.GenomicIterator source

usedFiles

java.lang.String[] usedFiles

Class gorsat.process.SourceProvider$ extends java.lang.Object implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Package gorsat.spark

Class gorsat.spark.GordFunction extends java.lang.Object implements Serializable

Serialized Fields

encoder

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

header

java.lang.String header

serializer

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

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

Class gorsat.spark.GorReaderFactory extends java.lang.Object implements Serializable

Serialized Fields

aliasFile

java.lang.String aliasFile

cacheDir

java.lang.String cacheDir

cacheFile

java.lang.String cacheFile

configFile

java.lang.String configFile

jobId

java.lang.String jobId

projectRoot

java.lang.String projectRoot

redisUri

java.lang.String redisUri

schema

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

securityContext

java.lang.String securityContext

streamKey

java.lang.String streamKey

useCpp

java.lang.String useCpp

Class gorsat.spark.GorSpecificInputPartition extends java.lang.Object implements Serializable

Serialized Fields

i

int[] i

j

int[] j

Class gorsat.spark.GorSpecificReaderFactory extends java.lang.Object implements Serializable

Package org.gorpipe.spark

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

Class org.gorpipe.spark.GorHeaderInferFunction extends java.lang.Object implements Serializable

Serialized Fields

convMap

java.util.Map<java.lang.String,java.lang.Character> convMap

Class org.gorpipe.spark.GorPartition extends java.lang.Object implements Serializable

Serialized Fields

p

int p

Class org.gorpipe.spark.GorPipeFunction extends java.lang.Object implements Serializable

Serialized Fields

cmd

java.lang.String cmd

header

java.lang.String header

Class org.gorpipe.spark.GorpipeRDD extends org.apache.spark.rdd.RDD<T extends java.lang.Object> implements Serializable

Serialized Fields

evidence$5

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

gor

boolean gor

header

java.lang.String header

org$gorpipe$spark$GorpipeRDD$$encoder

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

pipeStep

gorsat.Commands.Analysis pipeStep

Class org.gorpipe.spark.GorpWriter extends java.lang.Object implements Serializable

Serialized Fields

path

java.lang.String path

Class org.gorpipe.spark.GorQueryRDD extends org.apache.spark.rdd.RDD<java.lang.String> implements Serializable

Serialized Fields

aliasFile

java.lang.String aliasFile

allowFail

java.lang.Boolean[] allowFail

cacheDirectory

java.lang.String cacheDirectory

cacheFiles

java.lang.String[] cacheFiles

commandSignatures

java.lang.String[] commandSignatures

commandsToExecute

java.lang.String[] commandsToExecute

configFile

java.lang.String configFile

jobIds

java.lang.String[] jobIds

projectDirectory

java.lang.String projectDirectory

redisKey

java.lang.String redisKey

redisUri

java.lang.String redisUri

secCtxs

java.lang.String[] secCtxs

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

Serialized Fields

evidence$6

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

gor

boolean gor

gorcmd

java.lang.String gorcmd

header

java.lang.String header

Class org.gorpipe.spark.GorSparkArrayInferFunction extends java.lang.Object implements Serializable

Class org.gorpipe.spark.GorSparkRow extends SparkRow implements Serializable

Class org.gorpipe.spark.GorSparkRowBase extends org.gorpipe.gor.model.Row implements Serializable

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

Class org.gorpipe.spark.GorSparkRowInferFunction extends org.gorpipe.gor.function.GorRowInferFunction implements Serializable

Class org.gorpipe.spark.GorSparkRowMapFunction extends org.gorpipe.gor.function.GorRowMapFunction implements Serializable

Serialized Fields

schema

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

Class org.gorpipe.spark.GorSparkRowQueryFunction extends org.gorpipe.gor.function.GorRowQueryFunction implements Serializable

Class org.gorpipe.spark.Gorz extends java.lang.Object implements Serializable

Serialized Fields

block

java.lang.String block

CHROM

java.lang.String CHROM

POS

int POS

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.GorzFlatMap extends java.lang.Object implements Serializable

Serialized Fields

buffer

byte[] buffer

Class org.gorpipe.spark.GorzIterator extends java.lang.Object implements Serializable

Serialized Fields

header

java.lang.String header

Class org.gorpipe.spark.GorzStr extends java.lang.Object implements Serializable

Serialized Fields

block

java.lang.String block

CHROM

java.lang.String CHROM

POS

java.lang.String POS

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.HeaderFunction extends java.lang.Object implements Serializable

Serialized Fields

cmd

java.lang.String cmd

header

java.lang.String header

Class org.gorpipe.spark.HeaderInferFunction extends java.lang.Object implements Serializable

Serialized Fields

cmd

java.lang.String cmd

header

java.lang.String header

Class org.gorpipe.spark.LongGorSparkRow extends GorSparkRow implements Serializable

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

Class org.gorpipe.spark.NorSparkRow extends SparkRow implements Serializable

Class org.gorpipe.spark.NorSparkRowFilterFunction extends GorFilterFunction implements Serializable

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

Serialized Fields

filter

java.lang.String filter

gorcmd

java.lang.String gorcmd

Class org.gorpipe.spark.PipeFunction extends java.lang.Object implements Serializable

Serialized Fields

cmd

java.lang.String cmd

header

java.lang.String header

Class org.gorpipe.spark.QueryRDD extends org.apache.spark.rdd.RDD<java.lang.String> implements Serializable

Serialized Fields

cacheDir

java.lang.String cacheDir

commandSignatures

java.lang.String[] commandSignatures

commandsToExecute

java.lang.String[] commandsToExecute

hash

java.lang.String hash

header

boolean header

projectDirectory

java.lang.String projectDirectory

sparkSession

org.apache.spark.sql.SparkSession sparkSession

sqlContext

org.apache.spark.sql.SQLContext sqlContext

Class org.gorpipe.spark.Result extends java.lang.Object implements Serializable

Serialized Fields

ALT

java.lang.String ALT

CHROM

java.lang.String CHROM

ID

java.lang.String ID

M

java.lang.String M

POS

int POS

REF

java.lang.String REF

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

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

Class org.gorpipe.spark.SparkGOR.Dbsnp extends java.lang.Object implements Serializable

Serialized Fields

ALT

java.lang.String ALT

CHROM

java.lang.String CHROM

ID

java.lang.String ID

POS

int POS

REF

java.lang.String REF

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.SparkGOR.Gene extends java.lang.Object implements Serializable

Serialized Fields

chr

java.lang.String chr

end

int end

Gene_Symbol

java.lang.String Gene_Symbol

pos

int pos

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.SparkGOR.Skat extends java.lang.Object implements Serializable

Serialized Fields

chrom

java.lang.String chrom

numMarkers

int numMarkers

pvalue

java.lang.String pvalue

start

int start

stop

int stop

tag

java.lang.String tag

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.SparkGOR.Variants extends java.lang.Object implements Serializable

Serialized Fields

alt

java.lang.String alt

cc

int cc

chrom

java.lang.String chrom

cr

double cr

depth

int depth

filter

java.lang.String filter

formatZip

java.lang.String formatZip

fs

double fs

gl

int gl

pn

java.lang.String pn

pos

int pos

ref

java.lang.String ref

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.SparkGorMonitor extends org.gorpipe.gor.monitor.GorMonitor implements Serializable

Serialized Fields

jobId

java.lang.String jobId

Class org.gorpipe.spark.SparkGorMonitorFactory extends java.lang.Object implements Serializable

Class org.gorpipe.spark.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 extends java.lang.Object implements Serializable

Serialized Fields

age

long age

name

java.lang.String name

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

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class org.gorpipe.spark.SparkRow extends GorSparkRowBase implements Serializable

Serialized Fields

row

org.apache.spark.sql.Row row

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

Serialized Fields

gor

boolean gor

gorcmd

java.lang.String gorcmd

header

java.lang.String header

Package org.gorpipe.spark.udfs

Class org.gorpipe.spark.udfs.CharToDoubleArray extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArrayMissing extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArrayMissingParallel extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.CharToDoubleArrayParallel extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.CommaToDoubleArray extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.CommaToDoubleMatrix extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.CommaToIntArray extends java.lang.Object implements Serializable

Class org.gorpipe.spark.udfs.ListToVector extends java.lang.Object implements Serializable