Fixed major bug in data collection, provoking buffer overflow in
duplicate checking section. Now commented.
Added configuration flag to allow duplicate checking per read in data
collection.
Progressive read proccessing display in both recalibration phases.
Get data from one read function now works with an enviroment struct.
Fixed suppress_indels_from_32_cigar to work with limit array length.

This struct contains auxiliar arrays preallocated to avoid calling
malloc in this critical function.
Fixed null pointer check bug in getting data from bam.
Estimated quality is now stored in recalibration info (precalculated).
Recalibrate alignment no uses auxiliar enviroment like data collector.
Fixed bug when saving/loading estimated quality in recalibration info.