CHANGES IN VERSION 0.0.6 (10/06/2022)
-------------------------
1. Added the code in the function proteinLocsToProteinSeq() to deal
with the case that the input file contains some protein ID(s) which are not
in the gene annotation file and hence are not in the CDSaaFile used by the 
function. Accordingly, added one row at the end of the test data file
of the function
 transId_pfamDomainStartEnd_chr16_Zdomains_22examples_proteinID.txt 
for one protein ID which is not in any CDSaaFile in order to test the 
added code.
2. Made one change in the document Vignettes (in Section 1) to state that the 
package is in the CRAN repository.  


CHANGES IN VERSION 0.0.5 (06/02/2022)
-------------------------
1. Added the code in the function genomicLocsToProteinSequence() to deal
with the case that there is no overlap between the input genomic loci and the
protein coding genes, by returning a data frame with the genomic regions and 
result columns filled with NAs, instead of a short message.
2. Still in the function genomicLocsToProteinSequence(), it now outputs all the amino
acids coded by the DNA bases. In the previous version it did not output the amino acid coded 
by the last DNA bases if it needs some more DNA base after the current DNA sequences, which
looks not that intuitive.
3. Updated the introduction document (vignette) of the package.
4. Fixed an error caused by a new toolchain on Windows in which Perl installed on the system 
does not automatically convert newlines on input to LF. The fix method had been
proposed by the maintainers of CRAN repository who encountered the issue at the first place,
which was to replace all the "chomp;" in the two Perl scripts by "s/[\r\n]+//;".


CHANGES IN VERSION 0.0.4 (28/05/2018)
-------------------------
1. Added the code in the function genomicLocsToProteinSequence() to deal
with the case that there is no overlap between the input genomic loci and the
protein coding genes.  

CHANGES IN VERSION 0.0.3 (24/01/2018)
-------------------------
1. As the version 0.0.2 did not solve the issue of creating and writting some 
files in the folders that they should not be created, more modifications were done
in this version, namely putting the DNA sequence file uncompressed from the 
gz file to the temporary folder.


CHANGES IN VERSION 0.0.2 (23/01/2018)
-------------------------
1. Changed the function names of the two functions: genomicLocToProteinSequence 
-> genomicLocsToProteinSequence and genomicLocToWholeDNASequence -> 
genomicLocsToWholeDNASequence, in order to keep them consistent with other
function names.
2. Removed "utils" from the import list in DESCRIPTION file, because it is not
 used by the package.
3. Addressed the issue of creating and writting some files in the folders that
 they should not be created, as raised by the CRAN staff, by using the temporary
 folder obtained by tempdir(). 

-------------------------

VERSION 0.0.1

12/12/2017: the package was accepted and published by CRAN repository.
September - November 2017: the package was tested and reviewed.
January - May 2017: the package was written.
