Fixed bam indexing bug when -umi flag was used. Also refactored code into new way of getting stuff from config for picardExe
Fixed bam indexing bug when -umi flag was used. Also refactored code
into new way of getting stuff from config for picardExe

MonashBioinformaticsPlatform/RNAsik-pipe,MonashBioinformaticsPlatform/RNAsik-pipe,MonashBioinformaticsPlatform/RNAsik-pipe