Package net.maizegenetics.dna.map

Interface Summary

Interface	Description
GVCFGenomeSequence	Created by zrm22 on 3/27/17. Interface is used to store GenomeSequences defined by a GATK generated GVCF file
GenomeSequence	Defines the genome sequence of a chromosome
Position	Defines a genomic positions and its known variants. Includes attributes of chromosome, position, sub-position, strand, name (or SNP ID), whether this position is a nucleotide, or includes an indel.
PositionList	List of positions in the genome. This type is used by every interface GenotypeTable, but it can also be used list of GWAS results and other genomic annotations.
TOPMInterface	Tags on Physical Map (TOPM) Interface. Define methods for the TOPM classes. The TOPM class holds information relating tags to the physical map, variants (SNPs) called by the tag, and quality of mapping information.

Class Summary

Class	Description
AbstractPETagsOnPhysicalMap	Basic method of working with alignment of PE tags
AbstractTagsOnPhysicalMap	Abstract TagsOnPhysicalMap object. Abstract alignment is implemented by two types of TOPM classes class TagsOnPhysicalMap and class TagsOnPhysMapHDF5. TagsOnPhysicalMap is fully loaded into memory when read, and it can only support one mapping position (the files are either binary or text). TagsOnPhysMapHDF5 can support a large number of mapping position, and only a portion of the data is loaded into memory. In most cases, TagsOnPhysMapHDF5 should be preferred going forward.
Chromosome	Defines the chromosome structure and length. The name and length recorded for each chromosome.
DonorHaplotypes	Defines the haplotypes and positions of a chromosomal segment
GVCFGenomeSequenceBuilder	Created by zrm22 on 3/27/17.
GeneralPosition	Provide information on a site and its annotations. This includes information on position, MAF, coverage. This class is immutable.
GenomeFeature	Created by Jason Wallace on 7/2/14. This class stores a generic "feature" on a genome, such as a gene, transcript, exon, miRNA, etc. The intent is for this information to be read in from an external file (such as an Ensembl GFF/GTF file) and collated into a GenomeFeatureMap, but it could be used in other ways.
GenomeFeatureBuilder	Created by jgw87 on 7/2/14. Builder class to create a GenomeFeature. All annoations are stored in a HashMap. Any annotation can be added through the addAnnotation() method, but the more common fields have their own convenience methods. Only the feature's own ID is required; all other annotations are optional
GenomeFeatureMap	Created by jgw87 on 7/2/14. A map to hold genome features for lookup by name and by location. The features themselves are hierarchical and so can be traced up and down the tree.
GenomeFeatureMapBuilder	Created by jgw87 on 7/2/14. A Builder class to create a GenomeFeatureMap to identify genomic features. Can build piecemeal or read in from a file For now, not implementing functionality to make a new builder from an existing map.
GenomeSequenceBuilder	Builder for a chromosome genome sequence that hides the ReferenceGenomeSequence implementation. The sequence is read from a fasta file and stored in a byte array, 2 alleles packed per byte.
PETagsOnPhysicalMap
PETagsOnPhysicalMapV3	This class hold the multiple mapping positions of PE tags, including forward and backward PE tags. Data in this class are used to annotate HDF5TOPM When contig exist, the forward and backword tags are the contig and reverse complement of the contig, respectively. The PE tags were first aligned with bowtie2 (-k N), any number of mapping position can be imported PE tags of both end are stored in one long array with variable length, then they were truncated to 2 longs. This is easy for searching Using a pairIndex, each 64 bp tag has a index pointing to the other end of PE. It is worth noting that, the 64 bp tags are not unique. Rarely, there are multiple identical 64 bp tags, although the full length PE tags are unique. When multiple identical 64 bp tags exist, the one with longest full length PE is used to annotate HDF5TOPM.
PositionListBuilder	A builder for creating immutable PositionList. Can be used for either an in memory or HDF5 list.
PositionListIOUtils	Utilities for reading and writing Position Lists
PositionListTableReport
TOPMTableReport
TOPMUtils	Utility method for reading and writing TOPM files based on their file name suffixes.
TagGWASMap	Holding tag genetic mapping result from GWAS. It includes attributes and methods for machine learning prediction of mapping accuracy
TagGWASMapInfo	Stores variables from tag genetic mapping from GWAS. This class is used for I/O of HDF5.
TagGeneticMappingInfo	Class used to to store genetic mapping for hypothesis and output to H5 format
TagLocus	Aligns and calls SNPs for all tags at a given locus.
TagMappingInfo	Container class for information on mapping position.
TagMappingInfoV3	Container class for information on mapping position.
TagsOnGeneticMap	Class that hold genetic position of tags, genetic positions are the position of markers associated with tags
TagsOnPhysMapHDF5	HDF5 version of TagsOnPhysical Map. This is the preferred version of physical map as it uses less memory, loads faster, and is more flexible with mapping positions.
TagsOnPhysicalMap	Holds tag data compressed in long and a physical position. This can have two variations either include redundant positions or only unique positions. If redundant than tags that map to multiple regions should be placed adjacently Default 40 bytes per position. If we have 10,000,000 million positions then this will be at 400M byte data structure. User: ed
TagsOnPhysicalMapV3	HDF5 version of TagsOnPhysical Map. This is the preferred version of physical map as it uses less memory, loads faster, and is more flexible with mapping positions.
UpdateTOPMWithGeneticMapping	Update a physical map with genetic mapping information. The genetic mapping results would normally be derived from a run of TagCallerAgainstAnchorMT.