MAFToGVCF

Function to add a sequence Dictionary based on the reference genome. This uses the loaded genome to get the lengths.

Method to build an indel AssemblyVariantInfos.

Function to build a reference block AssemblyVariantInfo NucSeq is 0-based, so subtract 1 from the boundaries when grabbing the sequence allele

Method to build a Reference Block AssemblyVariantInfo setting the depth to 0. This is mainly used to fill in missing basepairs between MAF entries. NucSeq is 0-based, so subtract 1 from the boundary value when grabbing sequence allele

Method to build SNP AssemblyVariantInfos

Function to build the AssemblyVariantInfos found in the given Maf record.

Function to build the variants for all the alignments.

Function to turn the AssemblyVariantInfo into an actual VariantContext. If the Assembly annotations are not in the VariantInfo, we do not add them into the VariantContext.

This method takes a mafFile and outputs a gvcf file to the specified path

Function to export a list of htsjdk VariantContext records to a gvcf formatted output file

Function to fill in the missing variant blocks between MAF records. If fillWithRef is set to true it will make VariantBlocks, if false it will make missing blocks.

This function creates a list of MAFRecords records which will be further processed by the calling routing

Function to convert a multi-bp substitution into a series of SNPs. This allows the GVCF to pass a vcf-validator.

Method to resize the previous Reference block Variant Info. We only need to delete 1 bp off the end of the Blocks. We need to do this otherwise we will cover base pairs surrounding the indels.