Package: gmapR
Maintainer: Michael Lawrence <>
License: Artistic-2.0
Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
Type: Package
Author: Cory Barr, Thomas Wu, Michael Lawrence
Description: GSNAP and GMAP are a pair of tools to align short-read
        data written by Tom Wu.  This package provides convenience
        methods to work with GMAP and GSNAP from within R. In addition,
        it provides methods to tally alignment results on a
        per-nucleotide basis using the bam_tally tool.
Version: 1.19.0
Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
        GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
Imports: S4Vectors (>= 0.13.13), IRanges, 
        rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
        GenomicAlignments (>= 1.1.9), BiocParallel
Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
        GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
        GmapParam-class.R GsnapParam-class.R
        GsnapOutput-class.R GmapOutput-class.R
        atoiindex-command.R iit-format.R
        BamTallyParam-class.R bam_tally-command.R cmetindex-command.R
        get-genome-command.R gmap-command.R gmap_build-command.R
        gsnap-command.R iit_store-command.R info.R
        snpindex-command.R system.R test_gmapR_package.R
        makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
biocViews: Alignment