Did the #7 on the TODO list:
-included the reference to map to in the the samplefile
-several references can be mapped at the same time and the genome directories/indexes will be checked or made if needed for each
-remove the need to add datatype to add as a parameter and gets that information from the smplefile (based on the name of the sample)
-little differences here and there
Did the #7 on the TODO list: -included the reference to map to in the the samplefile -several references can be mapped at the same time and the genome directories/indexes will be checked or made if needed for each -remove the need to add datatype to add as a parameter and gets that information from the smplefile (based on the name of the sample) -little differences here and there