The GmapGenome class represents a genome that has been indexed for use with the GMAP suite of tools. It is typically used as a parameter to the functions gsnap and bam_tally. This class also provides the means to index new genomes, from either a FASTA file or a BSgenome object. Genome indexes are typically stored in a centralized directory on the file system and are identified by a string key.
The GmapGenomeDirectory class stores a path to a directory containing a one or more genome-specific subdirectories, each represented by a GmapGenome. Inside those directories are the files that the GMAP suite of tools uses for alignment, tallying, and other operations. This class is typically used to create a GmapGenome object. The default directory is ~/.local/share/gmap, following the freedesktop.org XDG standard.
This class represents a directory containig one or more sets of SNPs, each corresponding to a genome. These SNP databases enable SNP-tolerant alignment with GMAP and GSNAP. If the underlying files have not been created, this class provides a means to do so.
Returns a GmapGenome object consisting of the UCSC hg19 sequence centered on the region of the TP53 gene, with 1 Mb flanking sequence on each side. This is intended as a test/demonstration genome and can be used, e.g., in conjunction with the LungCancerLines data package.
Given a set of alignments, for each position in the genome output counts for the reference allele and all alternate alleles. Often used as a precursor to detecting variants. Indels will be supported soon.
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