importFrom(methods, new)
importFrom(SparseM, as.matrix, as.matrix.csr, t) 

importFrom(graphics, abline, legend, lines, par, plot, points)
importFrom(stats, chisq.test, dbinom, pbinom, rlnorm, rpois, runif)
importFrom(utils, data, read.table, write.table, unzip)

S3method(plot, sage.library)
S3method(plot, sage.library.comparison)
S3method(print, sage.library)
S3method(print, sage.library.comparison)
S3method(summary, sage.library)
S3method(summary, sage.library.comparison)
S3method(write, sage.library)
S3method(write, sage.library.comparison)


export(combine.libs, compare.lib.pair, compute.sequence.neighbors,
       compute.unique.tags, create.matrix.csr, difference.scatter.plot,
       em.estimate.error.given, estimate.errors.mean, extract.ditags,
       extract.lib.from.directory, extract.lib.from.zip, extract.library.tags,
       plot.sage.library, plot.sage.library.comparison, print.sage.library,
       print.sage.library.comparison, read.phd.file, read.sage.library,
       read.sage.library.comparison, read.seq.qual.filepair,
       reestimate.lib.from.tagcounts, remove.sage.artifacts, revcomp,
       sage.test, sagelibrary.simulate, summary.sage.library,
       summary.sage.library.comparison, table.sparse, tagmatrix2tagnum,
       tagnum2tagmatrix, tagnum2tagsequence, tagsequence2tagnum,
       write.sage.library, write.sage.library.comparison)
