TASSELpy.net.maizegenetics.dna.snp.genotypecall package¶

Submodules¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable module¶

class TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable.AbstractGenotypeCallTable(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable

Abstract implementation of methods in GenotypeCallTable

Methods

`alleleDefinitions`(*args)	Returns allele values as strings for all sites or for only one site.
`alleles`(*args)	Returns all alleles at given site in order of frequency.
`allelesSortedByFrequency`(*args)	Returns sorted list of alleles from highest frequency to lowest at given site in alignment.
`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`diploidAsString`(*args)	Returns String representation of diploid allele vlaue at site
`equals`(*args)	Indicates whether some other object is “equal to” this one
`genoCounts`(*args)	Returns counts of all diploid combinations from highest frequency to lowest for whole alignment.
`genosSortedByFrequency`(*args)	Return sorted list of diploid values from highest frequency to lowest at given site in alignment.
`genotype`(*args)	Returns diploid value (genotype) for a given taxon and site
`genotypeAllSites`(*args)	Returns sequence of diploid allele values for all sites for given taxon
`genotypeArray`(*args)	Returns the diploid values for given taxon and site
`genotypeAsString`(*args)	Returns string representation of diploid allele values returned by genotype() for given taxon and site.
`genotypeAsStringArray`(*args)	Returns string representation of diploid values returned by genotypeArray() for given taxon and site.
`genotypeAsStringRange`(*args)	Returns string representation of diploid alleles for given taxon in specified range (end site excluded).
`genotypeAsStringRow`(*args)	Returns string representation of diploid alleles for given taxon for all sites.
`genotypeForAllSites`(*args)	Get all genotypes for given taxon
`genotypeForAllTaxa`(*args)	Get all genotypes for given site
`genotypeForSiteRange`(*args)	Get all genotypes for given taxon from start site (inclusive) to end site
`genotypeRange`(*args)	Returns sequence of diploid allele values for given taxon in specified range (end site excluded).
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`hashCode`(*args)	Returns a hash code vlaue for the object
`heterozygousCount`(*args)	Returns the number of heterozygous taxa at given site
`heterozygousCountForTaxon`(*args)	Returns number of heterozygous sites at given taxon
`isAllPolymorphic`(*args)	Returns whether all sites are polymorphic
`isHeterozygous`(*args)	Returns whether allele values at given taxon and site are heterozygous.
`isPhased`(*args)	Returns whether this alignment is phased
`isPolymorphic`(*args)	Returns whether a given site is polymorphic
`majorAllele`(*args)	Returns most common allele at given site.
`majorAlleleAsString`(*args)	Returns most common allele at given site.
`majorAlleleCount`(*args)	Returns the major allele count for given site
`majorAlleleForAllSites`(*args)	Returns major allele for all sites
`majorAlleleFrequency`(*args)	Returns frequency for major allele at given site.
`majorMinorCounts`(*args)	Returns counts of all major/minor allele combinations from highest frequency to lowest for whole alignment.
`maxNumAlleles`(*args)	Return maximum number of alleles defined for any given site
`minorAllele`(*args)	Return most common minor allele at given site.
`minorAlleleAsString`(*args)	Return most common minor allele at given site.
`minorAlleleCount`(*args)	Returns the minor allele count for the given site
`minorAlleleForAllSites`(*args)	Returns minor allele for all sites
`minorAlleleFrequency`(*args)	Return frequency for the most common minor allele at given site.
`minorAlleles`(*args)	Return all minor alleles at given site.
`numberOfSites`(*args)	Returns number of sites in this genotype
`numberOfTaxa`(*args)	Returns number of taxa (samples) in this genotype
`retainsRareAlleles`(*args)	Returns true if this Alignment retains rare alleles.
`toString`(*args)	Returns a string representation of the object
`totalGametesNonMissingForSite`(*args)	Returns total number of non-missing allele values for given site.
`totalGametesNonMissingForTaxon`(*args)	Returns number of non-missing allele values for given taxon.
`totalNonMissingForSite`(*args)	Returns total number of non-missing taxa for given site.
`totalNonMissingForTaxon`(*args)	Returns total number of non-missing sites for given taxon.
`transposeData`(*args)	Tells this Genotype to transpose its data to optimize performance for given iteration nesting.
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

Abstract constructor for GenotypeCallTable

Signature:	AbstractGenotypeCallTable (int numTaxa, int numSites, boolean phased, String[][] alleleEncodings, int maxNumAlleles)
Signature:	AbstractGenotypeCallTable (int numTaxa, int numSites, boolean phased, String[][] alleleEncodings)

TASSELpy.net.maizegenetics.dna.snp.genotypecall.ByteGenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable module¶

class TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Interface for genotype calls for a table of taxa and sites. GenotypeCallTable only contain information on the genotype calls. The call table does not have the TaxaList or PositionList. The calls are diploid genotype calls stored and retrieved as bytes. Conversions to string are also provided.

Generally these methods are accessed through the GenotypeTable interface

Methods

`alleleDefinitions`(*args)	Returns allele values as strings for all sites or for only one site.
`alleles`(*args)	Returns all alleles at given site in order of frequency.
`allelesSortedByFrequency`(*args)	Returns sorted list of alleles from highest frequency to lowest at given site in alignment.
`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`diploidAsString`(*args)	Returns String representation of diploid allele vlaue at site
`equals`(*args)	Indicates whether some other object is “equal to” this one
`genoCounts`(*args)	Returns counts of all diploid combinations from highest frequency to lowest for whole alignment.
`genosSortedByFrequency`(*args)	Return sorted list of diploid values from highest frequency to lowest at given site in alignment.
`genotype`(*args)	Returns diploid value (genotype) for a given taxon and site
`genotypeAllSites`(*args)	Returns sequence of diploid allele values for all sites for given taxon
`genotypeArray`(*args)	Returns the diploid values for given taxon and site
`genotypeAsString`(*args)	Returns string representation of diploid allele values returned by genotype() for given taxon and site.
`genotypeAsStringArray`(*args)	Returns string representation of diploid values returned by genotypeArray() for given taxon and site.
`genotypeAsStringRange`(*args)	Returns string representation of diploid alleles for given taxon in specified range (end site excluded).
`genotypeAsStringRow`(*args)	Returns string representation of diploid alleles for given taxon for all sites.
`genotypeForAllSites`(*args)	Get all genotypes for given taxon
`genotypeForAllTaxa`(*args)	Get all genotypes for given site
`genotypeForSiteRange`(*args)	Get all genotypes for given taxon from start site (inclusive) to end site
`genotypeRange`(*args)	Returns sequence of diploid allele values for given taxon in specified range (end site excluded).
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`hashCode`(*args)	Returns a hash code vlaue for the object
`heterozygousCount`(*args)	Returns the number of heterozygous taxa at given site
`heterozygousCountForTaxon`(*args)	Returns number of heterozygous sites at given taxon
`isAllPolymorphic`(*args)	Returns whether all sites are polymorphic
`isHeterozygous`(*args)	Returns whether allele values at given taxon and site are heterozygous.
`isPhased`(*args)	Returns whether this alignment is phased
`isPolymorphic`(*args)	Returns whether a given site is polymorphic
`majorAllele`(*args)	Returns most common allele at given site.
`majorAlleleAsString`(*args)	Returns most common allele at given site.
`majorAlleleCount`(*args)	Returns the major allele count for given site
`majorAlleleForAllSites`(*args)	Returns major allele for all sites
`majorAlleleFrequency`(*args)	Returns frequency for major allele at given site.
`majorMinorCounts`(*args)	Returns counts of all major/minor allele combinations from highest frequency to lowest for whole alignment.
`maxNumAlleles`(*args)	Return maximum number of alleles defined for any given site
`minorAllele`(*args)	Return most common minor allele at given site.
`minorAlleleAsString`(*args)	Return most common minor allele at given site.
`minorAlleleCount`(*args)	Returns the minor allele count for the given site
`minorAlleleForAllSites`(*args)	Returns minor allele for all sites
`minorAlleleFrequency`(*args)	Return frequency for the most common minor allele at given site.
`minorAlleles`(*args)	Return all minor alleles at given site.
`numberOfSites`(*args)	Returns number of sites in this genotype
`numberOfTaxa`(*args)	Returns number of taxa (samples) in this genotype
`retainsRareAlleles`(*args)	Returns true if this Alignment retains rare alleles.
`toString`(*args)	Returns a string representation of the object
`totalGametesNonMissingForSite`(*args)	Returns total number of non-missing allele values for given site.
`totalGametesNonMissingForTaxon`(*args)	Returns number of non-missing allele values for given taxon.
`totalNonMissingForSite`(*args)	Returns total number of non-missing taxa for given site.
`totalNonMissingForTaxon`(*args)	Returns total number of non-missing sites for given taxon.
`transposeData`(*args)	Tells this Genotype to transpose its data to optimize performance for given iteration nesting.
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

alleleDefinitions(*args)[source]¶

Returns allele values as strings for all sites or for only one site. For the all sites definition, the first dimension of the array indexes the sites. The second dimension indexes the allele values for a given site. The indices for the allele vlaues are used as the codes to store data. These codes (indices) are returned by the genotypes() methods. If only one array of allele values is returned, that is the encoding for all sites

Signature:	alleleDefinitions ()
Signature:	alleleDefinitions (int site)
Parameters:	site (int) – site
Returns:	Allele values for given site
Return type:	String[][]

alleles(*args)[source]¶

Returns all alleles at given site in order of frequency. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts 2 for the allele value

Signature:	alleles (int site)
Parameters:	site (int) – site
Returns:	all alleles
Return type:	byte[]

allelesSortedByFrequency(*args)[source]¶

Returns sorted list of alleles from highest frequency to lowest at given site in alignment. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploidies are not supported

Signature:	allelesSortedByFrequency (int site)
Parameters:	site (int) – site
Returns:	Sorted list of alleles and counts
Return type:	int[][]

diploidAsString(*args)[source]¶

Returns String representation of diploid allele vlaue at site

Signature:	diploidAsString (int site, byte value)
Parameters:	site (int) – site value (byte) – diploid allele value
Returns:	String representation
Return type:	String

genoCounts(*args)[source]¶

Returns counts of all diploid combinations from highest frequency to lowest for whole alignment. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Longs)

Signature:	genoCount ()
Returns:	diploid counts
Return type:	Object[][]

genosSortedByFrequency(*args)[source]¶

Return sorted list of diploid values from highest frequency to lowest at given site in alignment. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Integers).

Signature:	genosSortedByFrequency (int site)
Parameters:	site (int) – site
Returns:	sorted list of diploids and counts
Return type:	Object[][]

genotype(*args)[source]¶

Returns diploid value (genotype) for a given taxon and site

Signature:	genotype (int taxon, int site)
Parameters:	taxon (int) – taxon site (int) – site
Returns:	High 4 bites generally encode the more frequent allele, and the lower 4 bits encode the less frequent allele
Return type:	byte

genotypeAllSites(*args)[source]¶

Returns sequence of diploid allele values for all sites for given taxon Each value in array is what would be returned by genotype()

Signature:	genotypeAllSites (int taxon)
Parameters:	taxon (int) – taxon
Returns:	Sequence of diploid allele values
Return type:	byte[]

genotypeArray(*args)[source]¶

Returns the diploid values for given taxon and site Same values as genotype(), except two values are already separated into two bytes

Signature:	genotypeArray (int taxon, int site)
Returns:	First byte (index 0) hold sfirst allele value in right-most 4 bits. Second byte (index 1) holds second value in right-most 4 bits
Return type:	byte[]

genotypeAsString(*args)[source]¶

Returns string representation of diploid allele values returned by genotype() for given taxon and site. The two allele values will be separated by a colon(:) delimiter

Signature:	genotypeAsString (int taxon, int site)
Signature:	genotypeAsString (int site, byte value)
Parameters:	taxon (int) – taxon site (int) – site value (byte) – diploid allele value
Returns:	String representation
Return type:	String

genotypeAsStringArray(*args)[source]¶

Returns string representation of diploid values returned by genotypeArray() for given taxon and site. Same 2 allele values as genotypeAsString(), except already separated into 2 Strings

Signature:	genotypeAsStringArray (int taxon, int site)
Parameters:	taxon (int) – taxon site (int) – site
Returns:	String representation of diploid vlaues
Return type:	String[]

genotypeAsStringRange(*args)[source]¶

Returns string representation of diploid alleles for given taxon in specified range (end site excluded). Each vlaue in string is what would be returned by genotypeAsString

Signature:	genotypeAsStringRange (int taxon, int startSite, int endSite)
Parameters:	taxon (int) – taxon startSite (int) – start site endSite (int) – end site
Returns:	String representation of alleles in range
Return type:	String

genotypeAsStringRow(*args)[source]¶

Returns string representation of diploid alleles for given taxon for all sites. Each value in string is what would be returned by genotypeAsString()

Signature:	genotypeAsStringRow (int taxon)
Parameters:	taxon (int) – taxon
Returns:	String representation of alleles
Return type:	String

genotypeForAllSites(*args)[source]¶

Get all genotypes for given taxon

Signature:	genotypeForAllSites (int taxon)
Parameters:	taxon (int) – taxon
Returns:	genotypes
Return type:	byte[]

genotypeForAllTaxa(*args)[source]¶

Get all genotypes for given site

Signature:	genotypeForAllTaxa (int site)
Parameters:	site (int) – site
Returns:	genotypes
Return type:	byte[]

genotypeForSiteRange(*args)[source]¶

Get all genotypes for given taxon from start site (inclusive) to end site (exclusive)

Signature:	genotypeForSiteRange (int taxon, int start, int end)
Parameters:	taxon (int) – taxon start (int) – start end (int) – end
Returns:	genotypes
Return type:	byte[]

genotypeRange(*args)[source]¶

Returns sequence of diploid allele values for given taxon in specified range (end site excluded). Each value in array is what would be returned by genotype().

Signature:	genotypeRange (int taxon, int startSite, int endSite)
Parameters:	taxon (int) – taxon startSite (int) – start site endSite (int) – end site
Returns:	sequence of diploid allele values
Return type:	byte[]

heterozygousCount(*args)[source]¶

Returns the number of heterozygous taxa at given site

Signature:	heterozygousCount (int site)
Parameters:	site (int) – site
Returns:	Number of heterozygous taxa
Return type:	int

heterozygousCountForTaxon(*args)[source]¶

Returns number of heterozygous sites at given taxon

Signature:	heterozygousCountForTaxon (int taxon)
Parameters:	taxon (int) – taxon
Returns:	number of heterozygous sites
Return type:	int

isAllPolymorphic(*args)[source]¶

Returns whether all sites are polymorphic

Signature:	isAllPolymorphic ()
Returns:	true if all sites are polymorphic
Return type:	boolean

isHeterozygous(*args)[source]¶

Returns whether allele values at given taxon and site are heterozygous. If 2 values returned by genotype() are different, this will return false

Signature:	isHeterozygous (int taxon, int site)
Parameters:	taxon (int) – taxon site (int) – site
Returns:	Whether heterozygous
Return type:	boolean

isPhased(*args)[source]¶

Returns whether this alignment is phased

Signature:	isPhased ()
Returns:	true if phased
Return type:	boolean

isPolymorphic(*args)[source]¶

Returns whether a given site is polymorphic

Signature:	isPolymorphic (int site)
Parameters:	site (int) – site
Returns:	true if given site is polymorphic
Return type:	boolean

majorAllele(*args)[source]¶

Returns most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous count 2 two for the allele value

Signature:	majorAllele (int site)
Parameters:	site (int) – site
Returns:	most common allele
Return type:	byte

majorAlleleAsString(*args)[source]¶

Returns most common allele at given site. Gap is included as state. Heterozygous count one for each allele vlaue. Homozygous counts 2 for the allele value

Signature:	majorAlleleAsString (int site)
Parameters:	site (int) – site
Returns:	most common allele as String
Return type:	String

majorAlleleCount(*args)[source]¶

Returns the major allele count for given site

Signature:	majorAlleleCount (int site)
Parameters:	site (int) – site
Returns:	major allele count
Return type:	int

majorAlleleForAllSites(*args)[source]¶

Returns major allele for all sites

Signature:	majorAlleleForAllSites ()
Returns:	all major alleles
Return type:	byte[]

majorAlleleFrequency(*args)[source]¶

Returns frequency for major allele at given site. Gap is included as state. Heterozygous count 1 for each allele value. Homozygous count 2 for the allele value

Signature:	majorAlleleFrequency (int site)
Parameters:	site (int) – site
Returns:	frequency
Return type:	double

majorMinorCounts(*args)[source]¶

Returns counts of all major/minor allele combinations from highest frequency to lowest for whole alignment. Resulting double dimension array holds major/minor allele (Strings) in result[0]. And the counts are in result[1] (Longs)

Signature:	majorMinorCounts ()
Returns:	diploid counts
Return type:	Object[][]

maxNumAlleles(*args)[source]¶

Return maximum number of alleles defined for any given site

Signature:	maxNumAlleles ()
Returns:	max number of alleles
Return type:	int

minorAllele(*args)[source]¶

Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts 2 for the allele value

Signature:	minorAllele (int site)
Parameters:	site (int) – site
Returns:	most common minor allele
Return type:	byte

minorAlleleAsString(*args)[source]¶

Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts 2 for the allele value

Arguments:

site – site

Returns:

Most common minor allele as String

minorAlleleCount(*args)[source]¶

Returns the minor allele count for the given site

Signatures:

int minorAlleleCount(int site)

Arguments:

site – site

Retuns:

minor allele count

minorAlleleForAllSites(*args)[source]¶

Returns minor allele for all sites

Signature:	minorAlleleForAllSites ()
Returns:	all minor alleles
Return type:	byte[]

minorAlleleFrequency(*args)[source]¶

Return frequency for the most common minor allele at given site. Gap is included as state. Heterozygous count 1 for each allele value. Homozygous count 2 for the allele value

Signature:	minorAlleleFrequency (int site)
Parameters:	site (int) – site
Returns:	frequency
Return type:	double

minorAlleles(*args)[source]¶

Return all minor alleles at given site.

Gap is included as state. Heterozygous count 1 for each allele value. Homozygous counts 2 for the allele value

Arguments:

site – site

Returns:

all minor alleles

numberOfSites(*args)[source]¶

Returns number of sites in this genotype

Signature:	numberOfSites ()
Returns:	number of sites
Return type:	int

numberOfTaxa(*args)[source]¶

Returns number of taxa (samples) in this genotype

Signature:	numberOfTaxa ()
Returns:	number of taxa
Return type:	int

retainsRareAlleles(*args)[source]¶

Returns true if this Alignment retains rare alleles. If false, rare alleles are recorded as unknown

Signature:	retainsRareAlleles ()
Returns:	Whether rare alleles are retained
Return type:	boolean

totalGametesNonMissingForSite(*args)[source]¶

Returns total number of non-missing allele values for given site. This can be twice the number of taxa, as diploid vlaues are supported

Signature:	totalGametesNonMissingForSite (int site)
Parameters:	site (int) – site
Returns:	number of non-missing allele values
Return type:	int

totalGametesNonMissingForTaxon(*args)[source]¶

Returns number of non-missing allele values for given taxon. This can be twice the number of sites, as diploid values are supported

Signature:	totalGametesNonMissingForTaxon (int taxon)
Parameters:	taxon (int) – taxon
Returns:	number of non-missing allele values
Return type:	int

totalNonMissingForSite(*args)[source]¶

Returns total number of non-missing taxa for given site. Taxa are considered missing only if both allele values are Unknown (N).

Signature:	totalNonMissingForSite (int site)
Parameters:	site (int) – site
Returns:	number of non-missing taxa
Return type:	int

totalNonMissingForTaxon(*args)[source]¶

Returns total number of non-missing sites for given taxon. Sites are considered missing only if both allele values are unknown (N).

Signature:	totalNonMissingForTaxon (int taxon)
Parameters:	taxon (int) – taxon

transposeData(*args)[source]¶

Tells this Genotype to transpose its data to optimize performance for given iteration nesting. If siteInnerloop is true, performance better when looping through sites inside taxa loop. If false, performance better when looping through taxa inside site loop

Signature:	transposeData (boolean siteInnerLoop)
Parameters:	siteInnerLoop (boolean) – flag for which iteration

TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule module¶

class TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule.GenotypeMergeRule(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Defines the methods for merging the calls from two taxa. The merge rules need to be defined at the level of genotypic calls and for read depth. In general, if depth is available, it will be used to merge

Methods

`callBasedOnDepth`(*args)	Makes a genotypic call based on allele depths
`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`hashCode`(*args)	Returns a hash code vlaue for the object
`isMergePossible`(*args)	Whether merge is even possible
`mergeCalls`(*args)	Merges diploid genotypic calls into one
`mergeWithDepth`(*args)	Merges sequencing depths of 2 taxa
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

callBasedOnDepth(*args)[source]¶

Makes a genotypic call based on allele depths

Signature:	callBasedOnDepth (byte[] genoDepths)
Parameters:	genoDepths (byte[]) – allele depth of taxa
Returns:	genotype call
Return type:	byte

isMergePossible(*args)[source]¶

Whether merge is even possible

Signature:	isMergePossible ()
Returns:	Whether merging is allowed
Return type:	boolean

mergeCalls(*args)[source]¶

Merges diploid genotypic calls into one

Signature:	mergeCalls (byte geno1, byte geno2)
Parameters:	geno1 (byte) – genotype call of taxa 1 geno2 (byte) – genotype call of taxa 2
Returns:	Merged genotype call
Return type:	byte

mergeWithDepth(*args)[source]¶

Merges sequencing depths of 2 taxa

Signature:	mergeWithDepth (byte[] geno1depths, byte[] geno2depths)
Parameters:	geno1depths (byte[]) – allele depths of taxa 1 geno2depths (byte[]) – allele depths of taxa 2
Returns:	merged depths
Return type:	byte[]

TASSELpy.net.maizegenetics.dna.snp.genotypecall package¶

Submodules¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.ByteGenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.NucleotideGenotypeCallTable module¶

Module contents¶

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TASSELpy.net.maizegenetics.dna.snp.genotypecall package¶

Submodules¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.ByteGenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule module¶

TASSELpy.net.maizegenetics.dna.snp.genotypecall.NucleotideGenotypeCallTable module¶

Module contents¶

Table Of Contents

This Page

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