THIS IS A API-INCOMPATIBLE CHANGE
Implement a speedup to the consensus_caller in UnifiedConsensusMaker.py
Uses a combination of Counters and cython to gain a 5x speedup in
consensus_caller, equating to a 2x speedup in overall operation of
UnifiedConsensusMaker.py, including UMI processing time.
Also makes use of a pysam function to more efficiently convert quality
scores into strings prior to write-out.
API-incompatible due to the use of Cython in the consensus_caller speedup.
THIS IS A API-INCOMPATIBLE CHANGE Implement a speedup to the consensus_caller in UnifiedConsensusMaker.py Uses a combination of Counters and cython to gain a 5x speedup in consensus_caller, equating to a 2x speedup in overall operation of UnifiedConsensusMaker.py, including UMI processing time. Also makes use of a pysam function to more efficiently convert quality scores into strings prior to write-out. API-incompatible due to the use of Cython in the consensus_caller speedup.