git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@61241 bc3139a8-67e5-0310-9ffc-ced21a209358
Cory Barr authored on 10/12/2011 01:00:07
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@@ -1,24 +1,23 @@ |
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Package: gmapR |
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-Type: Package |
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+Imports: Rsamtools (>= 1.7.4) |
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+Maintainer: <barr.cory@gene.com> |
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+License: Artistic-2.0 |
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Title: Provides convenience methods to work with GMAP and GSNAP from |
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within R |
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-Maintainer: <barr.cory@gene.com> |
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+Type: Package |
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Author: Cory Barr, 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 |
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to work with GMAP and GSNAP from within R |
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Version: 0.12.1 |
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-Depends: R (>= 2.14.0), tools, BiocGenerics (>= 0.1.3), IRanges (>= 1.13.8), |
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- rtracklayer (>= 1.15.3) |
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-Imports: Rsamtools (>= 1.7.4) |
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+Depends: R (>= 2.14.0), tools, BiocGenerics (>= 0.1.3), IRanges (>= |
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+ 1.13.8), rtracklayer (>= 1.15.3) |
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Suggests: RUnit |
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-License: Artistic-2.0 |
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-Collate: 'atoiindex.R' 'buildGmapDb.R' |
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- 'buildGmapDbSNPIndex.R' |
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+Collate: 'atoiindex.R' 'buildGmapDb.R' 'buildGmapDbSNPIndex.R' |
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'buildGmapIITFromFasta.R' 'buildGmapIndex.R' |
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'buildGmapSpliceSites.R' 'buildGsnapSNPIIT.R' |
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'buildRefseqSpliceSites.R' 'consolidateBAMFiles.R' |
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'consolidateGmapFiles.R' 'consolidateGsnapFiles.R' |
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'consolidateSAMFiles.R' 'exonsToGmapSpliceSites.R' |
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- 'getGsnapFileCounts.R' 'globals.R' 'gsnap.R' 'installGmap.R' |
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- 'parallelized_gsnap.R' 'test_gmapR_package.R' 'GsnapOutput-class.R' |
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+ 'getGsnapFileCounts.R' 'globals.R' 'GsnapOutput-class.R' 'gsnap.R' |
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+ 'installGmap.R' 'parallelized_gsnap.R' 'test_gmapR_package.R' |
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@@ -1,12 +1,3 @@ |
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-importFrom(tools, list_files_with_exts) |
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-import(BiocGenerics) |
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-importFrom(IRanges, isSingleString) |
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-importFrom(Rsamtools, bamPaths, path) |
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- |
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-export(GsnapOutput) |
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-exportClasses(GsnapOutput) |
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-exportMethods(bamPaths, path) |
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- |
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export(buildGmapDbSNPIndex) |
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export(buildGmapIITFromFasta) |
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export(buildGmapIndex) |
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@@ -29,8 +29,8 @@ buildGmapIITFromFasta <- function(genome, fasta, gmap_data_dir=NULL) {
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"-d", |
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genome) |
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if(!is.null(gmap_data_dir)) |
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- sys_command <- paste(sys_command, paste("-D",
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- file.path(gmap_data_dir, genome))) |
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+ sys_command <- paste(sys_command, |
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+ paste("-D", file.path(gmap_data_dir, genome)))
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sys_command <- paste(sys_command, fasta) |
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system(sys_command) |
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@@ -3,7 +3,7 @@ |
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\title{Download and Integrate dbSNP into GMAP/GSNAP}
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\usage{buildGmapDbSNPIndex(version)}
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\description{Downloads a version of dbSNP and integrates it into an installation of GMAP/GSNAP for SNP-tolerant alignment}
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-\details{.. content for details ..}
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+\details{.. content for \details{} ..}
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\value{0}
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\author{Cory Barr}
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\arguments{\item{version}{version of dbSNP to obtain}}
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similarity index 76% |
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rename from man/gsnapBuildRefseqSplicesites.Rd |
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rename to man/buildRefseqSpliceSites.Rd |
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@@ -1,7 +1,7 @@ |
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-\name{gsnapBuildRefseqSplicesites}
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-\alias{gsnapBuildRefseqSplicesites}
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+\name{buildRefseqSpliceSites}
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+\alias{buildRefseqSpliceSites}
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\title{Build RefSeq Splice Site IIT for gsnap}
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-\usage{gsnapBuildRefseqSplicesites(genome)}
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+\usage{buildRefseqSpliceSites(genome)}
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\description{add refSeq splice sites to gsnap}
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\details{downloads refSeq table from UCSC, parses out splice site donors
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and acceptors, creates IIT for gsnap, then copies IIT to genome's |