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

 Package: seqbias

-Version: 0.99.7

+Version: 0.99.8

 Date: 25-12-2010

 Title: Estimation of per-position bias in high-throughput sequencing data

 Description: This package implements a model of per-position sequencing bias in

new file mode 100644

@@ -0,0 +1,23 @@

+\name{seqbias}

+\docType{class}

+\alias{seqbias-class}

+

+\title{The seqbias model}

+

+\description{

+The \code{seqbias} class maintains a model of the sequencing bias of from an

+experiment, which can be saved, loaded, trained, and used to make predictions of

+bias.

+

+The class is manipulated with the following functions:

+\code{\link{seqbias.fit}}

+\code{\link{seqbias.load}}

+\code{\link{seqbias.predict}}

+\code{\link{seqbias.save}}

+}

+\author{

+    Daniel Jones

+    \email{dcjones@cs.washington.edu}

+}

+

+

@@ -1,11 +1,5 @@

-

 include Makevars.common

 OBJECTS = $(SEQBIAS_OBJ) \

 		  $(YAML_CPP_OBJ:%=yaml-cpp/%)

-all : $(SHLIB)

-

-clean:

-	rm -f $(OBJECTS)

-

@@ -1,10 +1,9 @@

-

-MYPKG_PATH=`echo 'cat(system.file("usrlib", \

-                      .Platform[["r_arch"]], \

-                      package="Rsamtools", mustWork=TRUE))' | \

-                  ${R_HOME}/bin/R --vanilla --slave`

-

-PKG_LIBS=-L$(MYPKG_PATH) -lbam

+SAMVARS=$(shell\

+  echo 'cat(system.file(\

+              "usretc", .Platform[["r_arch"]], "Rsamtools.mk",\

+               package="Rsamtools", mustWork=TRUE))' |\

+        "${R_HOME}/bin/R" --vanilla --slave)

+include $(SAMVARS)

 YAML_CPP_OBJ = aliascontent.o conversion.o emitter.o emitterstate.o \

                emitterutils.o exp.o iterator.o map.o node.o null.o \

@@ -17,7 +16,5 @@ SEQBIAS_OBJ = sequencing_bias.o kmers.o miscmath.o common.o \

 GNULIB_OBJ = asprintf.o printf-args.o printf-parse.o vasnprintf.o vasprintf.o

-DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64

-PKG_CFLAGS  += $(DFLAGS) -Wall

-PKG_CPPFLAGS = $(PKG_CFLAGS)

+PKG_CFLAGS  += -Wall

@@ -1,15 +1,5 @@

-

-PKG_LIBS+=-lws2_32

-PKG_CFLAGS+=-D_LARGEFILE64_SOURCE -DNEED_ASPRINTF

-

 include Makevars.common

-

+PKG_CPPFLAGS+=-DNEED_ASPRINTF

 OBJECTS = $(SEQBIAS_OBJ) \

 		  $(YAML_CPP_OBJ:%=yaml-cpp/%) \

 		  $(GNULIB_OBJ:%=gnulib/%)

-

-all : $(SHLIB)

-

-clean:

-	rm -f $(OBJECTS)

-