Serialized Form

Package uni.bielefeld.cmg.reflexiv.io

Class uni.bielefeld.cmg.reflexiv.io.ContigReader extends java.lang.Object implements Serializable

Serialized Fields

param
```
DefaultParam param
```
contigIDTable
```
java.util.HashMap<K,V> contigIDTable
```

contigPrimerTable

java.util.HashMap<K,V> contigPrimerTable

contigIDArray
```
java.lang.String[] contigIDArray
```
primerArray
```
java.lang.String[] primerArray
```

reflexivContigList

java.util.ArrayList<E> reflexivContigList

totalNum
```
int totalNum
```
name
```
java.lang.String name
```
contigId
```
int contigId
```
seq
```
java.lang.String seq
```
seqBuilder
```
java.lang.StringBuilder seqBuilder
```
info
```
InfoDumper info
```

Package uni.bielefeld.cmg.reflexiv.pipeline
- Class uni.bielefeld.cmg.reflexiv.pipeline.Pipelines extends java.lang.Object implements Serializable
  - Serialized Fields
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
    - outputBufferedWriter
```
java.io.BufferedWriter outputBufferedWriter
```
    - time
```
long time
```
- Class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivCounter extends java.lang.Object implements Serializable
  - Serialized Fields
    - time
```
long time
```
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivMain extends java.lang.Object implements Serializable
  - Serialized Fields
    - time
```
long time
```
    - param
```
DefaultParam param
```
    - info
```
InfoDumper info
```
- Class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivReAssembler extends java.lang.Object implements Serializable
  - Serialized Fields
    - time
```
long time
```
    - param
```
DefaultParam param
```
    - broadcastedPrimerArray
```
org.apache.spark.broadcast.Broadcast<T> broadcastedPrimerArray
```
    - info
```
InfoDumper info
```
Package uni.bielefeld.cmg.reflexiv.util
- Class uni.bielefeld.cmg.reflexiv.util.DefaultParam extends java.lang.Object implements Serializable
  - Serialized Fields
    - mightyName
```
java.lang.String mightyName
```
    - inputFqPath
```
java.lang.String inputFqPath
```
    - inputKmerPath
```
java.lang.String inputKmerPath
```
    - inputFaPath
```
java.lang.String inputFaPath
```
    - inputContigPath
```
java.lang.String inputContigPath
```
    - outputPath
```
java.lang.String outputPath
```
    - kmerSize
```
int kmerSize
```
    - subKmerSize
```
int subKmerSize
```
    - kmerBits
```
int kmerBits
```
    - kmerOverlap
```
int kmerOverlap
```
    - minReadSize
```
int minReadSize
```
    - minKmerCoverage
```
int minKmerCoverage
```
    - maxKmerCoverage
```
int maxKmerCoverage
```
    - minErrorCoverage
```
int minErrorCoverage
```
    - minContig
```
int minContig
```
    - bubble
```
boolean bubble
```
    - cache
```
boolean cache
```
    - partitions
```
int partitions
```
    - maximumIteration
```
int maximumIteration
```
    - minimumIteration
```
int minimumIteration
```
    - frontClip
```
int frontClip
```
    - endClip
```
int endClip
```
- Class uni.bielefeld.cmg.reflexiv.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.reflexiv.io

Class uni.bielefeld.cmg.reflexiv.io.ContigReader extends java.lang.Object implements Serializable

Serialized Fields

param

contigIDTable

contigPrimerTable

contigIDArray

primerArray

reflexivContigList

totalNum

name

contigId

seq

seqBuilder

info

Package uni.bielefeld.cmg.reflexiv.pipeline

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

Serialized Fields

param

info

outputBufferedWriter

time

Class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivCounter extends java.lang.Object implements Serializable

Serialized Fields

time

param

info

Class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivMain extends java.lang.Object implements Serializable

Serialized Fields

time

param

info

Class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivReAssembler extends java.lang.Object implements Serializable

Serialized Fields

time

param

broadcastedPrimerArray

info

Package uni.bielefeld.cmg.reflexiv.util

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

Serialized Fields

mightyName

inputFqPath

inputKmerPath

inputFaPath

inputContigPath

outputPath

kmerSize

subKmerSize

kmerBits

kmerOverlap

minReadSize

minKmerCoverage

maxKmerCoverage

minErrorCoverage

minContig

bubble

cache

partitions

maximumIteration

minimumIteration

frontClip

endClip

Class uni.bielefeld.cmg.reflexiv.util.InfoDumper extends java.lang.Object implements Serializable

Serialized Fields

message

mightyName