net.maizegenetics.dna.map

Class AbstractTagsOnPhysicalMap

AbstractTags

net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap

All Implemented Interfaces:

Tags, TOPMInterface

Direct Known Subclasses:

TagsOnPhysMapHDF5, TagsOnPhysicalMap, TagsOnPhysicalMapV3

public class AbstractTagsOnPhysicalMap
extends AbstractTags
implements TOPMInterface

Abstract TagsOnPhysicalMap object. Abstract alignment is implemented by two types of TOPM classes class TagsOnPhysicalMap and class TagsOnPhysMapHDF5. TagsOnPhysicalMap is fully loaded into memory when read, and it can only support one mapping position (the files are either binary or text). TagsOnPhysMapHDF5 can support a large number of mapping position, and only a portion of the data is loaded into memory. In most cases, TagsOnPhysMapHDF5 should be preferred going forward.

See Also:

class TagsOnPhysicalMap, class TagsOnPhysMapHDF5

Field Detail

bestChr

protected kotlin.Array[] bestChr

indicesOfSortByPosition

protected kotlin.Array[] indicesOfSortByPosition

myMaxVariants

protected int myMaxVariants

multimaps

protected kotlin.Array[] multimaps

bestStartPos

protected kotlin.Array[] bestStartPos

bestStrand

protected kotlin.Array[] bestStrand

myNumTags

protected int myNumTags

variantDefs

protected kotlin.Array[] variantDefs

variantOffsets

protected kotlin.Array[] variantOffsets

myChromosomes

protected kotlin.Array[] myChromosomes

myUniquePositions

protected kotlin.Array[] myUniquePositions

Constructor Detail

AbstractTagsOnPhysicalMap

public AbstractTagsOnPhysicalMap()

Method Detail

getMaxNumVariants

public int getMaxNumVariants()

getMultiMaps

public byte getMultiMaps(int index)

getChromosome

public int getChromosome(int index)

getSize

public int getSize()

getStartPosition

public int getStartPosition(int index)

getStrand

public byte getStrand(int tagIndex)

getVariantDef

public kotlin.Array[] getVariantDef()

getVariantDefByReference

protected kotlin.Array[] getVariantDefByReference()

Provides the reference

Returns:

org.jetbrains.dokka.NodeRenderContent@39d9e0f4:

getVariantOffByReference

protected kotlin.Array[] getVariantOffByReference()

getVariantDef

public byte getVariantDef(int tagIndex,
                          int variantIndex)

getVariantDefArray

public kotlin.Array[] getVariantDefArray(int tagIndex)

Returns an array containing all variant definitions for the tag at the supplied index.

Parameters:

tagIndex - tag index

Returns:

org.jetbrains.dokka.NodeRenderContent@6e29b75a: variant definitions for tag

getVariantOff

public kotlin.Array[] getVariantOff()

getVariantPosOff

public byte getVariantPosOff(int tagIndex,
                             int variantIndex)

getVariantPosOffArray

public kotlin.Array[] getVariantPosOffArray(int tagIndex)

Returns an array containing all variant position offsets for the tag at the supplied index.

Parameters:

tagIndex - tag index

Returns:

org.jetbrains.dokka.NodeRenderContent@1a03311b: variant position offsets for tag

printRow

public java.lang.String printRow(int row)

printWithMissing

public static java.lang.String printWithMissing(byte b)

printWithMissing

public static java.lang.String printWithMissing(int i)

writeTextFile

public void writeTextFile(java.io.File outfile)

getChromosomes

public kotlin.Array[] getChromosomes()

getChromosomeIndex

public int getChromosomeIndex(int intChrName)

getUniquePositions

public kotlin.Array[] getUniquePositions(int chromosome)

populateChrAndVarPositions

protected void populateChrAndVarPositions()

Creates the arrays for the all the positions for each chromosome as defined by the variants. Call this method after remapping or after loading the file, and it will be used for SNP calling.

getLoci

public Chromosome[] getLoci()

getLocus

public Chromosome getLocus(int tagIndex)

writeBinaryFile

public void writeBinaryFile(java.io.File outFile)

writeBinaryFile

protected void writeBinaryFile(java.io.File outFile,
                               boolean binary)

writeBinaryFile

public void writeBinaryFile(java.io.File outFile,
                            int minResolution,
                            boolean requirePhysPosition,
                            boolean requireDCOMap,
                            float minDCOP,
                            boolean binary)

TODO need to add LocusList to test, whether to include in output, move this to abstract

Parameters:

outFile -

minResolution -

requirePhysPosition -

requireDCOMap -

minDCOP -

binary -

writeBinaryFileForChromosomalRegion

public void writeBinaryFileForChromosomalRegion(java.io.File outFile,
                                                int targetChr,
                                                int minPos,
                                                int maxPos)

Outputs a new binary topm containing only tags with start positions that lie within the specified chromosomal region (inclusive). To obtain the whole chromosome, set minPos to Integer.MIN_VALUE and maxPos to Integer.MAX_VALUE TODO : generalize to other types of topm (HDF5, text)?

Parameters:

outFile - : use the suffix .topm

targetChr -

minPos - : set to Integer.MIN_VALUE for no cutoff

maxPos - : set to Integer.MAX_VALUE for no cutoff

mappedTags

public kotlin.Array[] mappedTags()

Returns:

org.jetbrains.dokka.NodeRenderContent@2f686dd6: An int[] result where : result[0] = The number of tags with a unique physical positions in this file (i.e. , tags for which the bestChr number is known). result[1] = The number of tags which align to multiple positions (i.e., where multimaps[tagIndex] > 0)

printRows

public void printRows(int numRows)

printRow

public java.lang.String printRow(int row,
                                 boolean byPosition)

printRows

public void printRows(int numRows,
                      boolean requirePhysPosition,
                      boolean byPosition)

printRows

public void printRows(int numRows,
                      boolean requirePhysPosition,
                      int printChr)

getTagsArray

protected kotlin.Array[] getTagsArray()

getTagLengthArray

protected kotlin.Array[] getTagLengthArray()