net.maizegenetics.pangenome.api

Class ConvertVariantContextToVariantInfo

net.maizegenetics.pangenome.api.ConvertVariantContextToVariantInfo

public class ConvertVariantContextToVariantInfo

Method Detail

convertContextToInfo

@NotNull
public static net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo convertContextToInfo(@NotNull
                                                                                                      htsjdk.variant.variantcontext.VariantContext variantContext,
                                                                                                      int gameteId)

Function to convert a VariantContext into a VariantInfo object. Need taxon and gamete id to get the correct genotype from the VariantContext. The gamete ID is used to get the correct allele for the genotype.

Using genotype position index instead of taxon. Otherwise converting context to info when processing consensus fails. Consensus has a list of taxon. originally we passed in the first one. But that could be "ref", and when processing the gvcf file we don't necessarily have ref in there, it may be the gvcf file for another line when they had the same data. Normally, "ref" would be chosen when taxa are equal. But for smallSeq, the ranking file ends up with Ref as first, so it gets rank 1, which is lowest.

convertGVCFContextToInfo

@NotNull
public static net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo convertGVCFContextToInfo(@NotNull
                                                                                                          htsjdk.variant.variantcontext.VariantContext variantContext,
                                                                                                          int gameteId)

convertVCListToVariantInfoList

@NotNull
public static java.util.List<net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo> convertVCListToVariantInfoList(@NotNull
                                                                                                                                java.util.List<? extends htsjdk.variant.variantcontext.VariantContext> variants,
                                                                                                                                @NotNull
                                                                                                                                java.lang.String taxon,
                                                                                                                                int gameteId)

Function to convert a list of variantContexts into a list of VariantInfos

convertGVCFListToVariantInfoList

@NotNull
public static java.util.List<net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo> convertGVCFListToVariantInfoList(@NotNull
                                                                                                                                  java.util.List<? extends htsjdk.variant.variantcontext.VariantContext> variants,
                                                                                                                                  int gameteId)

extractASMInfo

@NotNull
public static ASMVariantInfo extractASMInfo(@NotNull
                                                     htsjdk.variant.variantcontext.VariantContext variantContext)

isRefBlock

public static boolean isRefBlock(@NotNull
                                 htsjdk.variant.variantcontext.VariantContext gvcfRecord)

Helper function to check to see if a gvcf Record represents a reference block or just a single variant.

determineASMInfo

@NotNull
public static ASMVariantInfo determineASMInfo(@NotNull
                                                       java.util.List<? extends net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo> list,
                                                       int refRangeStart,
                                                       int refRangeEnd)