Serialized Form

Package uni.bielefeld.cmg.sparkhit.matrix
- Class uni.bielefeld.cmg.sparkhit.matrix.ScoreMatrix extends java.lang.Object implements Serializable
  - Serialized Fields
    - maxGapNum
```
int maxGapNum
```
    - maxNtTypes
```
int maxNtTypes
```
    - BLOSUM62
```
int[] BLOSUM62
```
    - gapArray
```
int[] gapArray
```
    - matrix
```
int[][] matrix
```
Package uni.bielefeld.cmg.sparkhit.pipeline
- Class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - pAlign
```
AlignmentParameter pAlign
```
    - BBList
```
java.util.List<E> BBList
```
    - listTitle
```
java.util.List<E> listTitle
```
    - index
```
KmerLoc[] index
```
    - mat
```
ScoreMatrix mat
```
    - totalLength
```
long totalLength
```
    - totalNum
```
int totalNum
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines extends java.lang.Object implements Serializable
  - Serialized Fields
    - threadName
```
java.lang.String threadName
```
    - inputFileBuffer
```
TextFileBufferInput inputFileBuffer
```
    - inputBufferedReader
```
java.io.BufferedReader inputBufferedReader
```
    - inputFastqUnitBuffer
```
FastqUnitBuffer inputFastqUnitBuffer
```
    - outputFileBuffer
```
TextFileBufferOutput outputFileBuffer
```
    - outputBufferedWriter
```
java.io.BufferedWriter outputBufferedWriter
```
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
    - processors
```
OnePipe[] processors
```
    - time
```
long time
```
    - ref
```
RefStructBuilder ref
```
    - matrix
```
ScoreMatrix matrix
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkBamPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
    - bamListReader
```
java.io.BufferedReader bamListReader
```
    - bamFile
```
java.util.List<E> bamFile
```
    - slides
```
int slides
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkChiSquarePipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkClusterPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkConvertPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkCorrelationPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkDecompressPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkHWEPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkParallelPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
    - data
```
java.util.List<E> data
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - time
```
long time
```
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkReductionPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkRegressionPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkReportPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.sparkhit.pipeline.SparkScriptPipe extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
Package uni.bielefeld.cmg.sparkhit.reference
- Class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - sizeKmers
```
int sizeKmers
```
    - alphaCode
```
int[] alphaCode
```
    - maximumKmerNum
```
int maximumKmerNum
```
    - info
```
InfoDumper info
```
    - BBList
```
java.util.List<E> BBList
```
    - block
```
java.util.List<E> block
```
    - title
```
java.util.List<E> title
```
    - index
```
KmerLoc[] index
```
    - totalLength
```
long totalLength
```
    - totalNum
```
int totalNum
```
    - name
```
java.lang.String name
```
    - length
```
int length
```
    - contigId
```
int contigId
```
    - seq
```
java.lang.String seq
```
    - seqBuilder
```
java.lang.StringBuilder seqBuilder
```
- Class uni.bielefeld.cmg.sparkhit.reference.RefStructSerializer extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - kSerializer
```
kryoSerializer kSerializer
```
    - jSerializer
```
JavaSerializer jSerializer
```
    - ref
```
RefStructBuilder ref
```
    - info
```
InfoDumper info
```
Package uni.bielefeld.cmg.sparkhit.struct
- Class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter extends java.lang.Object implements Serializable
  - Serialized Fields
    - maxReadLength
```
int maxReadLength
```
    - maxBlockLength
```
int maxBlockLength
```
    - oneNtBits
```
int oneNtBits
```
    - twoNtBits
```
int twoNtBits
```
    - threeNtBits
```
int threeNtBits
```
    - fourNtBits
```
int fourNtBits
```
    - maxNxM
```
int maxNxM
```
    - kmers
```
int[] kmers
```
    - revKmers
```
int[] revKmers
```
    - bRead
```
int[] bRead
```
    - bRevRead
```
int[] bRevRead
```
    - fourMer
```
int[] fourMer
```
    - fourMerBegin
```
int[] fourMerBegin
```
    - fourMerLoci
```
int[] fourMerLoci
```
    - fourMerScore
```
int[] fourMerScore
```
    - kmerHits
```
java.util.List<E> kmerHits
```
    - cRefBlockList
```
java.util.List<E> cRefBlockList
```
    - mergeRefBlockList
```
java.util.List<E> mergeRefBlockList
```
    - singleNtBit
```
int[] singleNtBit
```
    - singleNtBitComplement
```
int[] singleNtBitComplement
```
    - mRefBlockNtBit
```
int[] mRefBlockNtBit
```
    - scoreMatrix
```
int[][] scoreMatrix
```
    - alignLength
```
int alignLength
```
    - bestNas
```
int bestNas
```
    - bestKmers
```
int bestKmers
```
    - bestPigeon
```
int bestPigeon
```
    - fromFirst
```
int fromFirst
```
    - fromSecond
```
int fromSecond
```
    - endFirst
```
int endFirst
```
    - endSecond
```
int endSecond
```
    - align
```
int align
```
    - identityMatrix
```
int[][] identityMatrix
```
    - fromFirstMatrix
```
int[][] fromFirstMatrix
```
    - fromSecondMatrix
```
int[][] fromSecondMatrix
```
    - alignMatrix
```
int[][] alignMatrix
```
    - identity
```
int identity
```
    - bestScore
```
int bestScore
```
- Class uni.bielefeld.cmg.sparkhit.struct.BinaryBlock extends java.lang.Object implements Serializable
  - Serialized Fields
    - n
```
int n
```
    - s
```
int[] s
```
- Class uni.bielefeld.cmg.sparkhit.struct.Block extends java.lang.Object implements Serializable
  - Serialized Fields
    - id
```
int id
```
    - begin
```
int begin
```
    - end
```
int end
```
- Class uni.bielefeld.cmg.sparkhit.struct.CandidateBlock extends java.lang.Object implements Serializable
  - Serialized Fields
    - chr
```
int chr
```
    - end
```
int end
```
    - begin
```
int begin
```
- Class uni.bielefeld.cmg.sparkhit.struct.HitInfo extends java.lang.Object implements Serializable
  - Serialized Fields
    - chr
```
int chr
```
    - loc
```
int loc
```
- Class uni.bielefeld.cmg.sparkhit.struct.KmerLoc extends java.lang.Object implements Serializable
  - Serialized Fields
    - n
```
int n
```
    - id
```
int[] id
```
    - loc
```
int[] loc
```
- Class uni.bielefeld.cmg.sparkhit.struct.Qgram extends java.lang.Object implements Serializable
  - Serialized Fields
    - chr
```
int chr
```
    - begin
```
int begin
```
    - end
```
int end
```
    - qGrams
```
int qGrams
```
    - bandLeft
```
int bandLeft
```
    - bandRight
```
int bandRight
```
- Class uni.bielefeld.cmg.sparkhit.struct.QgramComparator extends java.lang.Object implements Serializable
- Class uni.bielefeld.cmg.sparkhit.struct.ReadInfo extends java.lang.Object implements Serializable
  - Serialized Fields
    - line
```
java.lang.String line
```
    - readName
```
java.lang.String readName
```
    - read
```
java.lang.String read
```
    - readSize
```
int readSize
```
    - r
```
readInfo r
```
- Class uni.bielefeld.cmg.sparkhit.struct.RefInfo extends java.lang.Object implements Serializable
  - Serialized Fields
    - refName
```
java.lang.String refName
```
    - refSize
```
long refSize
```
- Class uni.bielefeld.cmg.sparkhit.struct.RefTitle extends java.lang.Object implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
    - size
```
int size
```

Package uni.bielefeld.cmg.sparkhit.util

Class uni.bielefeld.cmg.sparkhit.util.DefaultParam extends java.lang.Object implements Serializable

Serialized Fields

mightyName
```
java.lang.String mightyName
```
inputBuildPath
```
java.lang.String inputBuildPath
```
inputResultPath
```
java.lang.String inputResultPath
```
word
```
java.lang.String word
```
count
```
int count
```
outputformat
```
int outputformat
```
inputFqPath
```
java.lang.String inputFqPath
```
inputTabPath
```
java.lang.String inputTabPath
```
inputFqLinePath
```
java.lang.String inputFqLinePath
```
inputFaPath
```
java.lang.String inputFaPath
```
filename
```
boolean filename
```
toolDepend
```
java.lang.String toolDepend
```
tool
```
java.lang.String tool
```
toolParam
```
java.lang.String toolParam
```
filterFastq
```
boolean filterFastq
```
filterToFasta
```
boolean filterToFasta
```
lineToFasta
```
boolean lineToFasta
```
window
```
int window
```
horizontal
```
boolean horizontal
```
columns
```
java.lang.String columns
```
columns2
```
java.lang.String columns2
```
columnStart
```
int columnStart
```
columnEnd
```
int columnEnd
```
column2Start
```
int column2Start
```
column2End
```
int column2End
```
clusterNum
```
int clusterNum
```
iterationNum
```
int iterationNum
```
model
```
int model
```
inputTrainPath
```
java.lang.String inputTrainPath
```
cache
```
boolean cache
```
componentNum
```
int componentNum
```
inputList
```
java.lang.String inputList
```
inputNodes
```
int inputNodes
```
outputPath
```
java.lang.String outputPath
```
threads
```
int threads
```
partitions
```
int partitions
```
kmerSize
```
int kmerSize
```
kmerBits
```
int kmerBits
```
maximumKmerNum
```
int maximumKmerNum
```
kmerOverlap
```
int kmerOverlap
```
bandWidth
```
int bandWidth
```
minReadSize
```
int minReadSize
```
maxReadSize
```
int maxReadSize
```
readIdentity
```
int readIdentity
```
globalOrLocal
```
int globalOrLocal
```
alignLength
```
int alignLength
```
reportRepeatHits
```
int reportRepeatHits
```
maskRepeat
```
int maskRepeat
```
validNt
```
java.util.regex.Pattern validNt
```
invalidNt
```
java.util.regex.Pattern invalidNt
```
validNtNomask
```
java.util.regex.Pattern validNtNomask
```
nxNomask
```
java.util.regex.Pattern nxNomask
```
bestKmers
```
int bestKmers
```
bestNas
```
int bestNas
```
bestPigeon
```
int bestPigeon
```
maxTrys
```
int maxTrys
```
skipThreshold
```
int skipThreshold
```
eValue
```
double eValue
```
chains
```
int chains
```
flagChains
```
char[] flagChains
```
codeNt
```
char[] codeNt
```
codeNtComplement
```
char[] codeNtComplement
```
alphaCode
```
int[] alphaCode
```
alphaCodeComplement
```
int[] alphaCodeComplement
```
alphaCodeNNNNN
```
int[] alphaCodeNNNNN
```
minor
```
double minor
```
lambda
```
double lambda
```
pairAlign
```
double pairAlign
```

Class uni.bielefeld.cmg.sparkhit.util.InfoDumper extends java.lang.Object implements Serializable
- Serialized Fields
  - message
```
java.lang.String message
```
  - mightyName
```
java.lang.String mightyName
```

Serialized Form

Package uni.bielefeld.cmg.sparkhit.matrix

Class uni.bielefeld.cmg.sparkhit.matrix.ScoreMatrix extends java.lang.Object implements Serializable

Serialized Fields

maxGapNum

maxNtTypes

BLOSUM62

gapArray

matrix

Package uni.bielefeld.cmg.sparkhit.pipeline

Class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe extends java.lang.Object implements Serializable

Serialized Fields

param

pAlign

BBList

listTitle

index

mat

totalLength

totalNum

Class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines extends java.lang.Object implements Serializable

Serialized Fields

threadName

inputFileBuffer

inputBufferedReader

inputFastqUnitBuffer

outputFileBuffer

outputBufferedWriter

param

info

processors

time

ref

matrix

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkBamPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

bamListReader

bamFile

slides

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkChiSquarePipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkClusterPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkConvertPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkCorrelationPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkDecompressPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkHWEPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkParallelPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

data

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe extends java.lang.Object implements Serializable

Serialized Fields

time

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkReductionPipe extends java.lang.Object implements Serializable

Serialized Fields

param

info

Class uni.bielefeld.cmg.sparkhit.pipeline.SparkRegressionPipe extends java.lang.Object implements Serializable