Cleanup of temporary SAM and BAM files
Merge pull request #10 from apetkau/fix/cleanup-files

Cleanup of temporary SAM and BAM files
Merge branch 'development'
fix bug where invalid position file was required and not optional
Merge pull request #11 from apetkau/development

fix bug where invalid position file was required and not optional when using --contig-dir
Merge branch 'master' into parallelization