Transform should not overwrite input files if output file would be produced with same name as input

[lonsbio]

From [email protected] on 2012-08-14T13:26:13Z

It's possible to construct a transform() that will make an output file the same name as an input file and destroy the input. eg:

transform("bam") {
exec "command $input.bed $input.bam > $output"
}

Bpipe should notice that the output file is going to have the same name as an input (or output from previous stage) and prevent that happening.

Original issue: http://code.google.com/p/bpipe/issues/detail?id=54