# 02/24/2014
# Changes made in the new (0.5) version of the TFTargetCaller package

1) "ensembl" changed to "geneID"
In the "gene" matrix the column containing gene IDs was named "ensembl". It was confusing because the user might wish to use other than Ensembl gene ID. In the current version "ensembl" has been changed to "geneID". All functions and documentiation have been changed accordingly.

2) Gene strand might be provided either as (1, -1) or as (+, -)
Before the "strand" column in the "gene" matrix had to be numeric and contain "1" for forward strain and "-1" for reverse strand. It was confusing because some users might use "+" and "-". Now the possibility of using "+" and "-" is enabled (they are automatically translated to 1 and -1, respectively). In addition, if the symbols in the "stand" column are neither (1, -1) nor (+, -) an error message is displayed.

3) An internal error allegedly related to the use of the "structure" function was corrected.

4) An internal error making the function crash when for any chromosome there was just one gene in the "gene" matrix was corrected.