Wed Mar 08 2006
  * correct bug with indexFasta(file) when file does not exists or
    when file like ~/file.fsa. 
  * indexEmbl indexGbk & indexFasta return -1 when error (to be 
    conform with makeIndex)

Mon Mar 06 2006
  * new function Match for "segSet" object.
  * and.segSet changed when used with one object.

Thu Mar 03 2006
  * posMaskedSeq(type="lower") renvoie numeric(0) au lieu de NULL

Wed Mar 01 2006
  * catch bug when use revComp(force=T).

Mon Feb 27 2006
  * optimize exactWord (not yet the optimum)
  * add warning message when access number too large with makeIndex
    functions.

Tue Feb 14 2006 GeneR_2.0.1
  * add parameter from and to to functions posMaskedSeq
    and posMaskedSeqFile
  * Use of 'absolute' addresses with function posMaskedSeq
    upperSeq and lowerSeq
	
Tue Jan 31 2006
  * Extend space for GBK & EMBL names in index files.
  * new allocation of GeneR sequences with stl vector container
  * new function readEmblDescript
  * getOrfs has a new parameter 'suborf'

Mon Jan 09 2006
  * add function bankSummary (that give a summay of a sequence bank
    file)
  * minor bug corrected in bankDensityProfile & dentityProfile
  * bug corrected in GCcontent
  * new param add to exactWord (overlap)

Mon Nov 28 2005
  * add flag complete for getOrfs and maxOrfs
  * allOrfs substitute by getOrfs
  * add function mask (that mask regions of a sequence)

Mon Nov 21 2005
  * delete psychedelic file abistr, abisys and ludglobal, functions
    move to file with intuitive file name.
  * seqSrs has no more option "fasta"
  * bug fixed to writeFasta for the comment when "complementaire"

Thu Nov 03 2005
  * bug fixed to function strreadFasta and C function alloc_char
  * new function strWriteFasta
  * new functions shuffleSeq and randomSeq
  * readEmblLocation and readGbkLocation rewritten

Fri Oct 28 2005
  * All C code rewritten in C++ 
  * delete function multiextract and strmultiextract (use getSeq and substr)
  * tuning of function densityProfile, bankDensityProfile GCcontent
    and seqSkew
  * ExactWord has a parameter case.sensitive
  * Delete function setEndSeq 
  * function getParam and setParam rewritten
  * readEmbl and readGbk has flag upper=F
  * readSeq, readFasta, readGbk, readEmbl sizeseq... has no more
    parameter path.
  * seqUrl rename to seqSrs
  * readGbkLocation and readEmblLocation removed.

Fri Oct 21 2005
  * As many buffers as needed (just change DEFINE MAX_BUFFER in file abisys_type.h)
  * fseek avoid for windows:
    fseek on windows count CR ('\r') and fgets does not see them
  * new function deleteCR 
  * Warning on makeIndex (for unix & mac) when a carriage return
    ('\r') found

Tue Oct 18 2005
  * modification in C file masked.c... so that posMaskedSeq function 
    gets last masked region if it ends sequence.
  * new function posMaskedSeqFile, and posMaskSeq works now on a
    bufseq and allow to find masked regions by 'N' or lower case...


Tue Oct 13 2005
  * strComp: uses lower cases
  * exactWord uses parameter strand instead of comp

Wed Oct 12 2005
  * add function appendSeq
  * add function upperSeq and lowerSeq
  * add flag force to function revComp
  * assemble debugged and has only a parameter strand (not p)  

Thu Oct  6 2005
  * add functions on intervals and segments.
  * placeString and readFasta has flag upper=TRUE
  * compoSeq ans strCompoSeq has flag case.

Thu Sep  1 2005: 1.3.1
  * all C functions pass with gcc -ansi flag.

Tue Aug 30 2005: 1.3.0
  * temporary remove intervals functions 
  * all C functions are declared, no more warnings with gcc -Wall 

Fri Aug 26 2005
  * remove unused functions from abistr.R and abistr.c 
  * remove function shuffle and all code from numerical reciepe

Tue Jun 09 2005
  * big changes in C function:
    + avoid long int (changed to int)
    + option upper for readFasta
    + check if EOF in all function on indexes.
    + new functions in vecteurs.c, not yet implemented in R.
  * writeFasta parameters reordered
  * minor changes in default parameters of assemble
  * new option upper = TRUE for readSeq and readFasta
  * unionSeq has now only one parameter
  * repercutions on demos and man pages

Tue Apr 12 2005
  * bug fixed to fastaDescription when description = ""

Tue Mar 08 2005
  * make indexes:
    + mini-check on type (embl, gbk, fasta)
    + makeIndex check if file newer than index (and then re-build index)
  * getSeq = multiExtract
  * add function unionSeg 

Thu Mar 03 2005
  * delete function mode ismodeabs, setMode...
  * exactWord returns begin of match when strand = 1
  * compoSeq gets values from 'absolute addresses' when strand = 1
    instead of 'real addresses'
  * Seed init modified with Shuffle

Web Feb 23 2005
  * Man pages re-organised
  * checksum disapear (will be on package digest)
  * functions w... and r... changed to set... and get... (rParam => getParam)

Fri Feb 11 2005
  * Bug fixed to allOrfs & maxOrfs in case: phase=NULL

Thu Feb 10 2005
  * new functions strReadEmbl / gbk / fasta
  * reorganization of files (and deletion of obsolete functions)

Thu Feb 03 2005 
  * new set of functions from protein translation
  * readEmbl & readGbk rewritten 
  * compoSeq rewritten and retrun matrix
  * new function strCompoSeq

Tue Jan 25 2005
  * R arguments are int => avoid long int in C functions...
  * main R functions use FreeSeq 
  * new function crc32

Thu Jan 20 2005
  * bug fixed with readGbkLocation
  * modif on allOrf, maxOrf, exactWord to give correct 
    errors messages
  * new function (aliases of readSeq)
    readEmbl, readFasta, readGbk
  * new function shuffle
  * readEmbl [a litle bit] optimized...

Wed Dec 12 2005
  * Normalised names
  * No more French in doc
  * name change to GeneR
  * maxOrf and allOrfs by default: find all phases
  * new function compoSeq & makeProfile

Mon Dec 10 2005
  * New functions WriteEMBL

Fri Dec 10 2004
  * abi.str.mutliextract supprime de abistr puisque ds abisys
  * idem pour abi.str.composeq!
  * idem pour abi.str.comp

Wed Dec 08 2004
  * begseq, endseq changed to from, to
  * seqncbi change to new parameters from ncbi...
  * write.fasta default values change

Thu Nov 18 2004
  * New function str2ascii => bug fixed to indexgbk embl ... 
  * New function read.fasta.description
  
Thu Oct 14 2004
  * Bug fixed in maxorf and allorfs:
    allorfs stops 2 nucleotids before
    maxorf gives 3 nucleotides less

Tue Oct 05 2004
  * bug fixed on maxorf (only seqno=0)

Wed Sep 15 2004
  * Minor Bug fixed to indexfasta (C function)
    ">" wasn't allowed in description field.

Tue Sep 14 2004
  * Bug fixed to readembl (do not write more than memory
    allocate)
  * Bug fixed to readembl (control the End of File)
  * Readembl is less restrictive to embl format:
    + new line tolerate in sequence list
    + numbers can be at the begining or the end of sequence
  * Bug fixed to indexfasta, embl , gbk (in sort part)
  * indexfasta, embl, gbk return 0 if error.

Mon Sep 06 2004
  * Add function write.fasta
  * minor changes for sequrl to compute version 7 of srs.

Thu Aug 19 2004
  * Minor changes to function sequrl and seqncbi while using
    option sousmotif=TRUE
    This option is usefull if we have ID too long like 
    dbj|BY608190.1|BY608190, given by ncbi.

Fri Aug 06 2004 BioR_0.1
  * All functions C has correct tags for Doxygen automatic
    documentation. => make inst/doc/index.html
  * minor bug fixed with complementaire function (alocate 1 
    character less).
  * more English documentation.

Tue Jul 27 2004 
  * sizeseqfasta embl gbk more simple (and do not look in
    directory /bk)
  * makeIndex do not make a  new index if exists.
  * readseq read.embl.location and read.gbk.location changes:
    + no more: name= file:accno, two fields file and accno
    + no more complicated thing directory /bk etc...
  * new functions sys_assemble concat from old package Bio-R

Mon Jul 26 2004 
  * abistr.R picked from old Bio-R package
  * No more double functions, and new functions from old Bio-R
    package: assemble, exactword rnddna concat ...
  * Makeindex and  readseq work for all type of bank
  * package=BioR for all C functions
  * new function AllORF indexgbk, indexfasta indexembl

Fri Jul 09 2004
  * Makeindex work without awk (C functions) for fasta bank

Fri Jul 02 2004
  * 1 less global variable in abisys.h 

Fri Apr 30 2004
  * new function read.embl.location

Wed Apr 28 2004
  * read.gbk.location work with any locus_tag or note or ....

Mon Apr 26 2004
  * initial Revision, minimal import from old package Bio-R
    for full compatibility.