#135 Move pacBio correction results to separate subdir(s)

[Harm van Bakel]

The cabog assembler has a clear directory structure, where each stage of the assembly ends up in its own subdir. In contrast, the final stages of pacBioToCA (runCorrection.sh and runPartition.sh) write all their output to the root of the temporary folder. When working with large genomes it is often convenient to rerun portions of the pipeline without repeating previous steps because they take too long (e.g. just run correctPacBio with different arguments). It would be a lot easier if the runCorrection and runPartition output was written to a separate subdir so that there is less chance of making mistakes when moving/deleting output files from a previous run.