setting up git-svn bridge

.Rinstignore

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+hiReadsProcessor_object.png
+hiReadsProcessor_workflow.png
+.DS_Store

DESCRIPTION

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+Package: hiReadsProcessor
+Title: Functions to process LM-PCR reads from 454/Illumina data.
+Version: 1.3.0
+Date: 2015-04-02
+Author: Nirav V Malani <[email protected]>
+Maintainer: Nirav V Malani <[email protected]>
+Description: hiReadsProcessor contains set of functions which allow
+        users to process LM-PCR products sequenced using any platform.
+        Given an excel/txt file containing parameters for
+        demultiplexing and sample metadata, the functions automate
+        trimming of adaptors and identification of the genomic product.
+        Genomic products are further processed for QC and abundance
+        quantification.
+Depends: Biostrings, GenomicAlignments, xlsx, BiocParallel,
+        hiAnnotator, R (>= 3.0)
+Imports: sonicLength, plyr, GenomicRanges, BiocGenerics, rSFFreader
+License: GPL-3
+VignetteBuilder: knitr
+Suggests: knitr, testthat
+biocViews: Sequencing, Preprocessing
+LazyLoad: yes
+SystemRequirements: BLAT, JRE, UCSC hg18 in 2bit format for BLAT

NAMESPACE

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+# Generated by roxygen2 (4.0.1): do not edit by hand
+
+export(addFeature)
+export(addListNameToReads)
+export(annotateSites)
+export(blatListedSet)
+export(blatSeqs)
+export(chunkize)
+export(clusterSites)
+export(crossOverCheck)
+export(decodeByBarcode)
+export(dereplicateReads)
+export(doRCtest)
+export(extractFeature)
+export(extractSeqs)
+export(findAndRemoveVector)
+export(findAndTrimSeq)
+export(findBarcodes)
+export(findIntegrations)
+export(findLTRs)
+export(findLinkers)
+export(findPrimers)
+export(findVector)
+export(getIntegrationSites)
+export(getSectorsForSamples)
+export(getSonicAbund)
+export(isuSites)
+export(otuSites)
+export(pairUpAlignments)
+export(pairwiseAlignSeqs)
+export(primerIDAlignSeqs)
+export(pslCols)
+export(pslToRangedObject)
+export(read.BAMasPSL)
+export(read.SeqFolder)
+export(read.blast8)
+export(read.psl)
+export(read.sampleInfo)
+export(read.seqsFromSector)
+export(removeReadsWithNs)
+export(replicateReads)
+export(sampleSummary)
+export(splitByBarcode)
+export(splitSeqsToFiles)
+export(startgfServer)
+export(trimSeqs)
+export(troubleshootLinkers)
+export(vpairwiseAlignSeqs)
+export(write.listedDNAStringSet)
+export(write.psl)
+import(BiocParallel)
+import(Biostrings)
+import(GenomicAlignments)
+import(hiAnnotator)
+import(plyr)
+import(sonicLength)
+import(xlsx)
+import(GenomicRanges)
+import(BiocGenerics)
+importFrom(rSFFreader,sread)
+importFrom(rSFFreader,readSff)
+

NEWS

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+hiReadsProcessor News
+
+CHANGES IN 1.1.3:
+  * Modified all bplapply calls
+  * Moved BiocGenerics and rSFFreader to Imports
+
+CHANGES IN 0.99.0:
+  * Added examples for almost all functions
+  * Removed Subread support
+
+CHANGES IN 0.3.35:
+  * Added annotateSites
+
+CHANGES IN 0.3.34:
+  * bug fix dereplicateReads & write.psl
+
+INITIALIZATION 0.3.33