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BARNA-212
Clean up class GraphLPsolverBARNA-211
LPSolverLoader assumes that libraries in the destination folder are correct, if identical by nameBARNA-209
Move KEEP_SORTED to File parameter
FluxCapacitor does not use sorted file for unsorted input if it already exists
FluxCapacitor deletes existing uncompressed BED file
FC output wrong strand information for countings
Gene Identifier preserved in GTF wrapper
FC need full path for output file on command line
BARNA-138
Implement BAM Reader to read BAM files
Capacitor Tests run into endless runs when GTF reader is not properly initialized (NULL pointer)
Line length is used instead of the mapping length for retrieving coverage stats within the learn() method
Add SAM/BAM support
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