Package: gmapR
Maintainer: Michael Lawrence <lawrence.michael@gene.com>
License: Artistic-2.0
Title: Provides convenience methods to work with GMAP and GSNAP from
    within R
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: 1.4.5
Depends: R (>= 2.15.0), methods, GenomicRanges
Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
         Biobase, BSgenome, methods
Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
	  BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,
          org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
          BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
License: Artistic-2.0
Collate: GmapBamReader-class.R
         GmapGenomeDirectory-class.R
         GmapGenome-class.R
         GmapSnpDirectory-class.R
         GmapSnps-class.R
         GsnapParam-class.R
         GsnapOutput-class.R
         atoiindex-command.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-format.R
         iit_store-command.R
         info.R
         snpindex-command.R
         system.R
         test_gmapR_package.R
         makeGmapGenomePackage.R
         TP53Genome.R
         utils.R
	 asSystemCall.R