added debug output. Moved clean up to end, so we maintain intermediate files in case of failure. Fixed bam deletion
added debug output. Moved clean up to end, so we maintain intermediate files in case of failure. Fixed bam deletion

Ensembl/ensembl-funcgen,Ensembl/ensembl-funcgen,Ensembl/ensembl-funcgen,Ensembl/ensembl-funcgen