Fix input file renaming regex

[eernst]

The previous regular expression caused problems with input filenames containing the substring "pp" because the "." characters in the pattern were not escaped. Also enforce the appearance of ".pp." just before the fastq or fq extensions.

[MichaelHiller]

Dear eernst,

thanks a lot for pointing out this problem. However, your bugfix still caused problems, e.g. in the cat command which would have created a single file containing the raw and preprocessed reads for indexing.

We have fixed the problem now by adding the string SGAICE to all temporary files. And the script error-exits in case the user inputs files that have this string.

Let us know if there are any other issues