net.maizegenetics.dna.map

Class TagsOnPhysMapHDF5

AbstractTags

AbstractTagsOnPhysicalMap

net.maizegenetics.dna.map.TagsOnPhysMapHDF5

All Implemented Interfaces:

Tags, TOPMInterface

public class TagsOnPhysMapHDF5
extends AbstractTagsOnPhysicalMap
implements TOPMInterface

HDF5 version of TagsOnPhysical Map. This is the preferred version of physical map as it uses less memory, loads faster, and is more flexible with mapping positions.

Multiple mapping positions can be stored for each Tag. For example, separate aligners could record their positions in the class TagMappingInfo objects. Then the genetic mapping algorithm could be used to resolve, which is the true mapping position. MapPosition0 is used as the best mapping position, and used by the SNP caller.

TODO: createFile - needs to instantiate a TOPM just using a Tag Object TODO: createFile that includes a Locus filter, only exports positions on the same locus and position range TODO: Resort map positions by quality

See Also:

class TagMappingInfo

Constructor Detail

TagsOnPhysMapHDF5

public TagsOnPhysMapHDF5(java.lang.String filename)

TagsOnPhysMapHDF5

public TagsOnPhysMapHDF5(java.lang.String theHDF5file,
                         boolean cacheAllMappingBlocks)

Method Detail

createFile

public static void createFile(AbstractTagsOnPhysicalMap inTags,
                              java.lang.String newHDF5file,
                              int maxMapping,
                              int maxVariants)

getFileReadyForClosing

public void getFileReadyForClosing()

getAlternateTagMappingInfo

public TagMappingInfo getAlternateTagMappingInfo(int index,
                                                 int mapIndex)

setAlternateTagMappingInfo

public void setAlternateTagMappingInfo(int index,
                                       int mapIndex,
                                       TagMappingInfo theTMI)

swapTagMappingInfo

public void swapTagMappingInfo(int index,
                               int mapIndex,
                               int mapIndex2)

addVariant

public int addVariant(int tagIndex,
                      byte offset,
                      byte base)

getDcoP

public byte getDcoP(int index)

getDivergence

public byte getDivergence(int index)

getEndPosition

public int getEndPosition(int index)

getMapP

public byte getMapP(int index)

getPositionArray

public kotlin.Array[] getPositionArray(int index)

getReadIndexForPositionIndex

public int getReadIndexForPositionIndex(int posIndex)

getUniquePositions

public kotlin.Array[] getUniquePositions(int chromosome)

setMultimaps

public void setMultimaps(int index,
                         byte multimaps)

setChromoPosition

public void setChromoPosition(int index,
                              int chromosome,
                              byte strand,
                              int positionMin,
                              int positionMax)

setDivergence

public void setDivergence(int index,
                          byte divergence)

setMapP

public void setMapP(int index,
                    byte mapP)

setMapP

public void setMapP(int index,
                    double mapP)

setVariantDef

public void setVariantDef(int tagIndex,
                          int variantIndex,
                          byte def)

setVariantPosOff

public void setVariantPosOff(int tagIndex,
                             int variantIndex,
                             byte offset)

setAllVariantInfo

public void setAllVariantInfo(int tagIndex,
                              kotlin.Array[] defAndOffset)

Preferred method for setting variant information

Parameters:

tagIndex -

defAndOffset - Two dimension [0=definition, 1=offset][upto 16 bytes for each SNP]

clearVariants

public void clearVariants()