net.maizegenetics.dna.tag

Interface PETags

All Known Implementing Classes:

AbstractPETags, AbstractPETagsOnPhysicalMap, PETagCounts, PETagsOnPhysicalMap

public PETags

Basic interface for holding sets of sequence tag (these are compressed into 2-bit codings of tags). The length of tag in good sequence is also tracked.

Method Detail

getTagSizeInLong

int getTagSizeInLong()

Returns the number of long use to represent the sequence

Returns:

org.jetbrains.dokka.NodeRenderContent@46dc8865: Tag Length in Long primitive data type

getTagFLength

short getTagFLength(int index)

Returns the length in bp of a forward tag

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@628d0231: length of the forward tag

getTagBLength

short getTagBLength(int index)

Returns the length in bp of a backward tag

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@4cd02438: length of the backward tag

getTagF

kotlin.Array[] getTagF(int index)

Get the compressed forward tag sequence in a long array for a given index

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@4d7496d0: compressed forward tag sequence in long array

getTagB

kotlin.Array[] getTagB(int index)

Get the compressed backward tag sequence in a long array for a given index

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@6fc9b0bb: compressed backward tag sequence in long array

getTagIndex

int getTagIndex(kotlin.Array[] tagF,
                kotlin.Array[] tagB)

Gets the index of a PE tag (including forward and backward) (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.

Parameters:

tagF - Long array of forward tag

tagB - Long array of backward tag

Returns:

org.jetbrains.dokka.NodeRenderContent@655fbbf9: index of the PE tag

getTagCount

int getTagCount()

This is the number of different PE tags in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct tags if readUnique is true

Returns:

org.jetbrains.dokka.NodeRenderContent@28e3b28e: total number of tags

getContig

kotlin.Array[] getContig(int index)

Return the contig of PE tag

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@41487354: Contig of a PE tag, if there is no contig, return null

getContigCount

int getContigCount()

Return total number of PE contigs

Returns:

org.jetbrains.dokka.NodeRenderContent@63a64fae: Total count of PE Contig

getContigLength

short getContigLength(int index)

Return the length of a contig

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@7b3eb050: PE contig length

getContigLengthInLong

byte getContigLengthInLong(int index)

Return the contig length in Long primitive data type

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@4efc0a7b: contig length in Long primitive data type