DESCRIPTION
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 Package: gmapR
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 Maintainer: Michael Lawrence <michafla@gene.com>
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 License: Artistic-2.0
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 Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
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 Type: Package
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 Author: Cory Barr, Thomas Wu, Michael Lawrence
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 Description: GSNAP and GMAP are a pair of tools to align short-read
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         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.
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 Version: 1.36.0
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
         rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings,
         VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome,
         GenomicAlignments (>= 1.15.6), BiocParallel
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 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
         LungCancerLines
 Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
         GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
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         GmapParam-class.R GsnapParam-class.R
         GsnapOutput-class.R GmapOutput-class.R
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         atoiindex-command.R iit-format.R
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         BamTallyParam-class.R bam_tally-command.R cmetindex-command.R
         get-genome-command.R gmap-command.R gmap_build-command.R
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         gsnap-command.R iit_store-command.R info.R
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         snpindex-command.R system.R test_gmapR_package.R
         makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
 biocViews: Alignment