net.maizegenetics.analysis.phg

Class ParseGVCF.GVCFLine

net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine

Enclosing class:

ParseGVCF

public static class ParseGVCF.GVCFLine

Constructor Detail

GVCFLine

public GVCFLine(int lineNum,
                java.lang.String line)

Method Detail

lineNum

public int lineNum()

Line number in the .g.vcf file

Returns:

org.jetbrains.dokka.NodeRenderContent@3c4e1e49: line number

toString

public java.lang.String toString()

chromosome

public java.lang.String chromosome()

startPosition

public int startPosition()

Start physical position (inclusive)

Returns:

org.jetbrains.dokka.NodeRenderContent@480ff690: start physical position

endPosition

public int endPosition()

End physical position (inclusive)

Returns:

org.jetbrains.dokka.NodeRenderContent@5c444415: end physical position

seqLength

public int seqLength()

Length of sequence represented by this line

Returns:

org.jetbrains.dokka.NodeRenderContent@699b9467: sequence length

depth

public int depth()

Total depth

Returns:

org.jetbrains.dokka.NodeRenderContent@25eb634b: depth

alleleDepths

public java.util.List<java.lang.Integer> alleleDepths()

isHomozygous

public boolean isHomozygous()

reference

public java.lang.String reference()

Returns:

org.jetbrains.dokka.NodeRenderContent@1267aa10: reference http://samtools.github.io/hts-specs/VCFv4.2.pdf REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String. For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event; this padding base is not required (although it is permitted) for e.g. complex substitutions or other events where all alleles have at least one base represented in their Strings. If any of the ALT alleles is a symbolic allele (an angle-bracketed ID String) then the padding base is required and POS denotes the coordinate of the base preceding the polymorphism. Tools processing VCF files are not required to preserve case in the allele Strings. (String, Required).

alternates

public java.util.List<java.lang.String> alternates()

Returns:

org.jetbrains.dokka.NodeRenderContent@6cfd20a5: alternate base(s) http://samtools.github.io/hts-specs/VCFv4.2.pdf ALT - alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,*, (case insensitive) or an angle-bracketed ID String or a breakend replacement string as described in the section on breakends. The ‘*’ allele is reserved to indicate that the allele is missing due to a upstream deletion. If there are no alternative alleles, then the missing value should be used. Tools processing VCF files are not required to preserve case in the allele String, except for IDs, which are case sensitive. (String; no whitespace, commas, or angle-brackets are permitted in the ID String itself)

genotypeIndices

public java.util.List<java.lang.Integer> genotypeIndices()

Returns:

org.jetbrains.dokka.NodeRenderContent@59f0a9f1: genotype http://samtools.github.io/hts-specs/VCFv4.2.pdf GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1 | 0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, ‘.’ should be specified for each missing allele in the GT field (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes): / : genotype unphased | : genotype phased

genotypes

public java.util.List<java.lang.String> genotypes()

phased

public boolean phased()

ploidy

public int ploidy()

isReferenceBlock

public boolean isReferenceBlock()

Returns whether this line specifies a range of positions that match the reference.

Returns:

org.jetbrains.dokka.NodeRenderContent@277f78bf: whether this is a reference block