Package vcf
Class BasicGTRec
java.lang.Object
vcf.BasicGTRec
- All Implemented Interfaces:
IntArray
,DuplicatesGTRec
,GTRec
,MarkerContainer
Class BasicGTRec
stores genotypes for a list of samples
at a single marker. The phased or unphased status of each genotype is
stored.
Instances of class BasicGTRec
are immutable.
-
Constructor Summary
ConstructorsConstructorDescriptionBasicGTRec
(VcfRecGTParser recParser) Constructs a newBasicGTRec
instance representing the specified VCF record's GT format field data. -
Method Summary
Modifier and TypeMethodDescriptionint
allele1
(int sample) Returns the first allele for the specified sample or -1 if the allele is missing.int
allele2
(int sample) Returns the second allele for the specified sample or -1 if the allele is missing.int[]
alleles()
Returns an array of lengththis.size()
whosej
-th element is equal tothis.allele(j
}int
get
(int hap) Returns the specified allele for the specified haplotype or -1 if the allele is missing.boolean
isPhased()
Returnstrue
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise.boolean
isPhased
(int sample) Returnstrue
if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.marker()
Returns the marker.samples()
Returns the list of samples.int
size()
Returns the number of haplotypes.toString()
Returns the data represented bythis
as a VCF record with a GT format field.
-
Constructor Details
-
BasicGTRec
Constructs a newBasicGTRec
instance representing the specified VCF record's GT format field data.- Parameters:
recParser
- the VCF record genotype data- Throws:
IllegalArgumentException
- if a format error is detected in the VCF recordNullPointerException
- ifrecParser == null
-
-
Method Details
-
samples
Description copied from interface:GTRec
Returns the list of samples. -
size
public int size()Description copied from interface:DuplicatesGTRec
Returns the number of haplotypes.- Specified by:
size
in interfaceDuplicatesGTRec
- Specified by:
size
in interfaceIntArray
- Returns:
- the number of haplotypes
-
marker
Description copied from interface:MarkerContainer
Returns the marker.- Specified by:
marker
in interfaceMarkerContainer
- Returns:
- the marker
-
isPhased
public boolean isPhased()Description copied from interface:DuplicatesGTRec
Returnstrue
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Returns:
true
if the genotype for each sample is a phased, non-missing genotype
-
isPhased
public boolean isPhased(int sample) Description copied from interface:DuplicatesGTRec
Returnstrue
if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Parameters:
sample
- a sample index- Returns:
true
if the genotype for the specified sample is a phased, nonmissing genotype
-
allele1
public int allele1(int sample) Description copied from interface:DuplicatesGTRec
Returns the first allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.- Specified by:
allele1
in interfaceDuplicatesGTRec
- Parameters:
sample
- a sample index- Returns:
- the first allele for the specified sample
-
allele2
public int allele2(int sample) Description copied from interface:DuplicatesGTRec
Returns the second allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.- Specified by:
allele2
in interfaceDuplicatesGTRec
- Parameters:
sample
- a sample index- Returns:
- the second allele for the specified sample
-
get
public int get(int hap) Description copied from interface:DuplicatesGTRec
Returns the specified allele for the specified haplotype or -1 if the allele is missing. The two alleles for a sample at a marker are arbitrarily ordered ifthis.unphased(marker, hap/2) == false
.- Specified by:
get
in interfaceDuplicatesGTRec
- Specified by:
get
in interfaceIntArray
- Parameters:
hap
- a haplotype index- Returns:
- the specified allele for the specified sample
-
alleles
public int[] alleles()Description copied from interface:DuplicatesGTRec
Returns an array of lengththis.size()
whosej
-th element is equal tothis.allele(j
}- Specified by:
alleles
in interfaceDuplicatesGTRec
- Returns:
- an array of length
this.size()
whosej
-th element is equal tothis.allele(j
}
-
toString
Returns the data represented bythis
as a VCF record with a GT format field. The returned VCF record will have missing QUAL and INFO fields, will have "PASS" in the filter field, and will have a GT format field.
-