net.maizegenetics.dna.read

Class Read

net.maizegenetics.dna.read.Read

public class Read

Class holding reads of Fastq format.

Constructor Detail

Read

public Read(java.lang.String ID,
            java.lang.String seq,
            java.lang.String des,
            java.lang.String qual)

Method Detail

returnAverageQuality

public byte returnAverageQuality(int phredScale)

Return average quality value of read

Returns:

org.jetbrains.dokka.NodeRenderContent@73f38421:

getMedianQuality

public byte getMedianQuality(int phredScale)

Return median quality of read

Returns:

org.jetbrains.dokka.NodeRenderContent@41a8ca1a:

getReadLength

public int getReadLength()

Return read length

Returns:

org.jetbrains.dokka.NodeRenderContent@5be85313:

getBaseQuality

public byte getBaseQuality(int index,
                           int phredScale)

Return quality value of base

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@1a219dc:

getDescription

public java.lang.String getDescription()

Return description of read

Returns:

org.jetbrains.dokka.NodeRenderContent@6e9f4745:

getID

public java.lang.String getID()

Return ID of read

Returns:

org.jetbrains.dokka.NodeRenderContent@69e0b896:

getSeq

public java.lang.String getSeq()

Return read

Returns:

org.jetbrains.dokka.NodeRenderContent@70090e72:

getReverseQual

public java.lang.String getReverseQual()

Return reverse quality string

Returns:

org.jetbrains.dokka.NodeRenderContent@61748556:

getQual

public java.lang.String getQual()

Return quality string

Returns:

org.jetbrains.dokka.NodeRenderContent@75c55352:

getQual

public java.lang.String getQual(int startIndex,
                                int endIndex)

Return quality string from startIndex to endIndex

Parameters:

startIndex -

endIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@198d6174:

getSeq

public java.lang.String getSeq(int startIndex,
                               int endIndex)

Return read from startIndex to endIndex

Parameters:

startIndex -

endIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@214f96a9:

getReverseComplementarySeq

public java.lang.String getReverseComplementarySeq()

Return reverse complementary sequence

Returns:

org.jetbrains.dokka.NodeRenderContent@6454f9e3:

getReverseComplementarySeq

public java.lang.String getReverseComplementarySeq(int startIndex,
                                                   int endIndex)

Return reverse complementary sequence

Parameters:

startIndex - inclusive

endIndex - exclusive

Returns:

org.jetbrains.dokka.NodeRenderContent@3bd469f8: