Here is a list of all file members with links to the files they belong to:

- r -

• R : codon.h
• RangeLess() : Range.cpp
• RangeLessPtr() : Range.cpp
• rcbase() : kzseq.cpp
• rcsid : dna.cpp
• RCSID : misc.h
• rcsid : encoding.cpp , align.cpp , misc.cpp , prnt.cpp , args.cpp , sim4b1.cpp , sim4main.cpp , discrim.cpp , splice.cpp , Xtend1.cpp
• read() : subcluster.cpp
• readAbinitioModel() : caiwe.cpp
• readAcc() : picknewseq.cpp
• readAlnFromArchive() : combest.cpp
• readAlnFromOneArchive() : combest.cpp
• readandstoreGmap() : GenModel.cpp , GenModel.h
• readandstoreSam() : combest.cpp
• readConf() : seqdiv.cpp
• readconf() : doublestop.cpp
• readConfig() : combest.cpp , dbaln.cpp
• readESTModel() : caiwe.cpp
• readGFSR() : GFSR.c , GFSR.h
• readgfsr_() : GFSR.c
• readId() : caiwe.cpp
• readIdFromFasta() : estlibcount.cpp
• readIdList() : estlibcount.cpp
• readIndex() : kzseq.cpp , kzseq.h
• reading() : README
• readJGIModel() : caiwe.cpp
• readSeqFromFile() : uniqueshortseq.cpp
• readStat() : rmfalselink.cpp
• readStatInt() : rmfalselink.cpp
• readSumm() : blpur.cpp
• readUnwantedTaxid() : chimeradetect_mysql.cpp
• red : Esambl.h
• Reduction10() : oldbionj.c
• Reduction4() : oldbionj.c
• refineAllmodels() : doublestop.cpp
• refineLoci() : combest.cpp
• refType : ref.h
• releaseAbinitioModel() : caiwe.cpp
• releaseESTModel() : caiwe.cpp
• releaseJGIModel() : caiwe.cpp
• releaseMemory() : estlibcount.cpp , gathercaiwegene.cpp , gathergene.cpp
• releaseResult() : estlibcount.cpp
• releaseVectorMemory() : combest.cpp
• relink() : sim4b1.cpp
• remove_end_mark() : util.cpp , util.h
• remove_nrjunk() : footprintHelper.cpp , footprintHelper.h , pickrepmodel.cpp
• removeChimeraModels() : nrep.cpp
• removeDoneFile() : nrep.cpp
• removeFalsePositiveHits() : rmfalselink.cpp
• removeIdentical() : nrep.cpp
• removeLowCDSModels() : nrep.cpp
• removePregnantModels() : nrep.cpp
• removeSimilarModels() : combest.cpp
• removeSimple() : uniqueshortseq.cpp
• removeSimpleMatch() : chimeradetect_mysql.cpp
• removeSingleExonModel() : combest.cpp
• replace() : util.cpp , util.h
• replaceInnerQuote() : util.cpp , util.h
• replQuote() : head.cpp
• resolve_overlap() : sim4b1.cpp
• results_init() : results_init.c , alnfn.h
• resultType() : blpurify.cpp
• retainIntron() : astyping.cpp
• revcomp() : helper.h , helper.c , helper.h
• reverse_list() : helper.c , helper.h
• reverseCompareResult() : GenModel.cpp
• reverseComplement() : bioseq.cpp , bioseq.h
• reverseComplementInPlace() : bioseq.cpp , bioseq.h
• reverseEdit() : GenModel.cpp
• revseq() : helper.c , helper.h
• rmAuthorPunc() : ref.cpp
• rmdquote() : strformat.h , strformat.cpp , strformat.h , strformat.cpp
• rmJournalDot() : ref.cpp
• rmsp() : strformat.cpp , strformat.h , strformat.cpp , strformat.h , strformat.cpp
• rmsp1() : strformat.cpp
• rmspace() : util.h , util.cpp
• rmtsp() : strformat.cpp , strformat.h
• RNA : RNAModel.h
• RNASEQ : bioseq.h
• rpldquote() : strformat.cpp , strformat.h , strformat.cpp , strformat.h , strformat.cpp , strformat.h
• rpt_align() : aln_output.h , aln_output.c
• rpt_alignment() : aln_output.c , aln_output.h
• rpt_row() : aln_output.h , aln_output.c
• rpt_scores() : aln_output.h , aln_output.c , aln_output.h
• rpt_version() : helper.c , helper.h
• rsnake() : align.cpp
• run : README
• rwComment() : g2a.cpp