Remove old files

[JoseBlanca]

It would be nice to have the chance to remove the files that won't be needed anymore when an analysis is done. In that way a lot of disk space could be saved. For instance the different verions of the annotation database are useless.

Not all the files used should be considered old, though. For instance raw reads shouldn't because they have information, like extra low quality reads, not present in the cleaned reads.

This behaviour should be configurable in the configuration file by a parameter in the general section called remove_old_file. Should this parameter set be default to True or to False?

The implementation could be a method in the Analysis class named clean_old_reads. The daugther classes could reimplemented. Alternatively this reinplementation could be saved if the files to remove are defined in the analyses description like the input and output files are. In that way the method in the Analysis class could take care in most cases.

[pziarsolo]

What happend with bam files. At the moment we have three merged bam files:
merge analysis, realign analysis and calmd analysis. Plus the bams for each read file.