Package vcf
Interface GTRec
- All Superinterfaces:
DuplicatesGTRec
,IntArray
,MarkerContainer
- All Known Subinterfaces:
RefGTRec
- All Known Implementing Classes:
BasicGTRec
,BitArrayGTRec
,BitArrayRefGTRec
,LowMafDiallelicGTRec
,LowMafGTRec
,LowMafRefDiallelicGTRec
,LowMafRefGTRec
,SeqCodedRefGTRec
,VcfRec
Interface GTRec
represents represents genotype data for one
marker.
All instances of GTRec
are required to be immutable.
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Method Summary
Modifier and TypeMethodDescriptionstatic int[]
alleleCounts
(GTRec rec) Returns the allele counts.static double[]
alleleFreq
(GTRec rec) Returns the allele frequencies.samples()
Returns the list of samples.static String
Returns a VCF record corresponding to the specifiedGTRec
object.Methods inherited from interface vcf.DuplicatesGTRec
allele1, allele2, alleles, get, isPhased, isPhased, size
Methods inherited from interface vcf.MarkerContainer
marker
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Method Details
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samples
Samples samples()Returns the list of samples.- Returns:
- the list of samples
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alleleFreq
Returns the allele frequencies. Thek
-th element of the returned array is the frequency of thek
-th allele.- Parameters:
rec
- the genotype data for a marker- Returns:
- the allele frequencies
-
alleleCounts
Returns the allele counts. Thek
-th element of the returned array is the count of thek
-th allele.- Parameters:
rec
- the genotype data for a marker- Returns:
- the allele frequencies
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toVcfRec
Returns a VCF record corresponding to the specifiedGTRec
object. 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.- Parameters:
gtRec
- the genotype data- Returns:
- a VCF record corresponding to the specified
GTRec
object - Throws:
NullPointerException
- ifgtRec == null
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