@@ -15,7 +15,7 @@ Depends: R (>= 2.15.0), methods, GenomicRanges

 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, pasillaBamSubset, 

-	  BSgenome.Scerevisiae.UCSC.sacCer3

+	  BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation

 License: Artistic-2.0

 Collate: GmapBamReader-class.R

          GmapGenomeDirectory-class.R

@@ -23,11 +23,9 @@ importClassesFrom(VariantAnnotation, "VCF")

 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,

        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,

-       flankingCycleBreaks)

+       GmapSnps, GmapSnpDirectory)

+

 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,

               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)

-exportMethods(bamPaths, path, genome, seqinfo, gsnap)

-

-## gsnap API

-## export("snps<-", getDefaultGmapGenomePath)

+exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-")

@@ -28,6 +28,13 @@ test_GmapGenome_constructor_BSgenome_create <- function() {

   checkTrue(is(gmapGenome, "GmapGenome"))

 }

+testGmapGenome_constructor_FastaFile_create <- function() {

+  fa <- system.file("extdata/hg19.p53.fasta", package="gmapR", mustWork=TRUE)

+  fastaFile <- rtracklayer::FastaFile(fa)

+  gmapGenome <- GmapGenome(fastaFile, create=TRUE)

+  checkTrue(is(gmapGenome, "GmapGenome"))

+}

+

 test_GmapGenome_accessors <- function() {

   genomeName <- "testGenome"

   dna <- Biostrings::DNAStringSet("ACTGTGTCAG")

@@ -77,6 +77,12 @@ flyGG <- GmapGenome(Dmelanogaster, create = TRUE)

 ## access system-wide genome using a key

 flyGG <- GmapGenome(genome = "dm3",

                     directory = path.expand("/usr/share/gmap"))

+

+##create a GmapGenome from a FASTA file

+fa <- system.file("extdata/hg19.MT.fasta", package="gmapR")

+fastaFile <- rtracklayer::FastaFile(fa)

+gmapGenome <- GmapGenome(fastaFile, create=TRUE)

 }

+

 }

 \keyword{classes}

@@ -3,6 +3,7 @@

 \docType{class}

 \alias{GmapSnps-class}

 \alias{directory,GmapSnps-method}

+\alias{GmapSnps}

 \title{Class \code{"GmapSnps"}}

 \description{

@@ -14,6 +15,29 @@

 Objects can be created by calls of the form \code{GmapSnps(snps,

   directory, name, create)}.

 }

+

+\usage{GmapSnps(snps, directory, name = snps, create = FALSE, ...)}

+

+\arguments{

+  \item{snps}{A path to a VCF file}

+  \item{directory}{The directory to create the IIT files used by GMAP

+  and GSNAP}

+  \item{name}{If provided, the name to give the database of SNPs. If not

+  provided, defauts to the \code{snps} argument.}

+  \item{create}{If the directory provided in the \code{directory}

+  argument does not exist, create it.}

+  }

+  

+\section{Accessors}{

+    \describe{

+      \item{}{\code{name(x)}: returns the name of the \code{GmapSnps} object}

+      \item{}{\code{directory(x)}: returns the \code{GmapGenomeDirectory}

+	that is the parent of the directory containing the index files for

+	this \code{GmapSnps} object.}

+    }

+}

+

+  

 \section{Methods}{

   \describe{

     \item{directory}{\code{signature(x = "GmapSnps")}: ... }

@@ -38,7 +38,6 @@ destDir = ".", license = "Artistic-2.0", pkgName)

 \examples{

 \dontrun{

-

 library(gmapR)

 if (!require(BSgenome.Dmelanogaster.UCSC.dm3)) {

@@ -1,5 +1,8 @@

 /* src/config.h.in.  Generated from configure.ac by autoheader.  */

+/* Define if building universal (internal helper macro) */

+#undef AC_APPLE_UNIVERSAL_BUILD

+

 /* Define to 1 if bsr command is available in assembly */

 #undef HAVE_ASM_BSR

@@ -221,9 +224,17 @@

 /* Version number of package */

 #undef VERSION

-/* Define to 1 if your processor stores words with the most significant byte

-   first (like Motorola and SPARC, unlike Intel and VAX). */

-#undef WORDS_BIGENDIAN

+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most

+   significant byte first (like Motorola and SPARC, unlike Intel). */

+#if defined AC_APPLE_UNIVERSAL_BUILD

+# if defined __BIG_ENDIAN__

+#  define WORDS_BIGENDIAN 1

+# endif

+#else

+# ifndef WORDS_BIGENDIAN

+#  undef WORDS_BIGENDIAN

+# endif

+#endif

 /* Number of bits in a file offset, on hosts where this is settable. */

 #undef _FILE_OFFSET_BITS

@@ -1,6 +1,9 @@

 /* src/config.h.  Generated from config.h.in by configure.  */

 /* src/config.h.in.  Generated from configure.ac by autoheader.  */

+/* Define if building universal (internal helper macro) */

+/* #undef AC_APPLE_UNIVERSAL_BUILD */

+

 /* Define to 1 if the system has the type `caddr_t'. */

 #define HAVE_CADDR_T 1

@@ -146,7 +149,7 @@

 #define HAVE_ZLIB 1

 /* Define to 1 if your zlib library has a gzbuffer function. */

-#define HAVE_ZLIB_GZBUFFER 1

+/* #undef HAVE_ZLIB_GZBUFFER */

 /* Define to the sub-directory in which libtool stores uninstalled libraries.

    */

@@ -203,9 +206,17 @@

 /* Version number of package */

 #define VERSION "2012-07-06"

-/* Define to 1 if your processor stores words with the most significant byte

-   first (like Motorola and SPARC, unlike Intel and VAX). */

-/* #undef WORDS_BIGENDIAN */

+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most

+   significant byte first (like Motorola and SPARC, unlike Intel). */

+#if defined AC_APPLE_UNIVERSAL_BUILD

+# if defined __BIG_ENDIAN__

+#  define WORDS_BIGENDIAN 1

+# endif

+#else

+# ifndef WORDS_BIGENDIAN

+/* #  undef WORDS_BIGENDIAN */

+# endif

+#endif

 /* Enable large inode numbers on Mac OS X 10.5.  */

 #ifndef _DARWIN_USE_64_BIT_INODE

@@ -1,5 +1,8 @@

 /* src/config.h.in.  Generated from configure.ac by autoheader.  */

+/* Define if building universal (internal helper macro) */

+#undef AC_APPLE_UNIVERSAL_BUILD

+

 /* Define to 1 if the system has the type `caddr_t'. */

 #undef HAVE_CADDR_T

@@ -202,9 +205,17 @@

 /* Version number of package */

 #undef VERSION

-/* Define to 1 if your processor stores words with the most significant byte

-   first (like Motorola and SPARC, unlike Intel and VAX). */

-#undef WORDS_BIGENDIAN

+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most

+   significant byte first (like Motorola and SPARC, unlike Intel). */

+#if defined AC_APPLE_UNIVERSAL_BUILD

+# if defined __BIG_ENDIAN__

+#  define WORDS_BIGENDIAN 1

+# endif

+#else

+# ifndef WORDS_BIGENDIAN

+#  undef WORDS_BIGENDIAN

+# endif

+#endif

 /* Enable large inode numbers on Mac OS X 10.5.  */

 #ifndef _DARWIN_USE_64_BIT_INODE

@@ -295,6 +295,61 @@ After creating the package, you can run \Rcode{R CMD INSTALL

   myDestDir} to install it, or run \Rcode{R CMD build myDestDir} to

 create a distribution of the package.

+Many users with be working with the human genome. Many of the examples

+used in \software{gmapR} make use of a particular build of the human

+genome. As such, creating a \Rclass{GmapGenome} of hg19 is

+recommended. Here is one way to create it, using a \Rclass{BSgenome}

+object:

+

+<<create_hg19_GmapGenome, eval=FALSE>>=

+if (!suppressWarnings(require(BSgenome.Hsapiens.UCSC.hg19))) {

+  source("http://bioconductor.org/biocLite.R")

+  biocLite("BSgenome.Hsapiens.UCSC.hg19")

+  library(BSgenome.Hsapiens.UCSC.hg19)

+}

+gmapGenome <- GmapGenome(genome=Hsapiens,

+                         directory = "Hsapiens",

+                         name = "hg19",

+                         create = TRUE)

+destDir <- "HsapiensGmapGenome"

+pkgName <- "GmapGenome.Hsapiens.UCSC.hg19"

+makeGmapGenomePackage(gmapGenome=gmapGenome,

+                      version="1.0.0",

+                      maintainer="<your.name@somewhere.com>",

+                      author="Your Name",

+                      destDir=destDir,

+                      license="Artistic-2.0",

+                      pkgName="GmapGenome.Hsapiens.UCSC.hg19")

+@ 

+

+After running the above code, you should be able to run \Rcode{R CMD

+  INSTALL GmapGenome.Hsapiens.UCSC.hg19} in the appropriate directory

+from the command line, submit GmapGenome.Hsapiens.UCSC.hg19 to a

+repository, etc. After installation,

+\Rcode{library("GmapGenome.Hsapiens.UCSC.hg19")} will load a

+\Rclass{GmapGenome} object that has the same name as the package.

+

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

+\section{Aligning with SNP Tolerance}

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

+

+Both \software{GSNAP} and \software{GMAP} have the ability to perform

+alignment without penalizing against a set of known SNPs. In this

+section, we work through an example of aligning with this SNP

+tolerance. By using SNP-tolerance, we'll perform alignments without

+penalizing reads that match SNPs contained in the provided SNPs. In

+this case, we'll use dbSNP to provide the SNPs.

+

+This example will use hg19. If you have not installed

+\Rcode{GmapGenome.Hsapiens.UCSC.hg19}, please refer to the section

+\ref{create_hg19_GmapGenome}.

+

+First we load the Hsapiens \Rclass{GmapGenome} object:

+

+<<<load_GmapGenomeHsapiens>>=

+library("GmapGenome.Hsapiens.UCSC.hg19")

+@ 

+

 <<SessionInfo>>=

 sessionInfo()

 @