Added dataStructs to iterate over hash
Sorting hash functionality
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
GT-97 - added converage profiles and fixed issue with overlap calculation
Added merged gene body coverage
Exclude unpaired single end reads from gene counts by default
Fixed coverage conter
Cleanup and reverse transcript support for coverage counts
Fixed the coverage conters
GT-97 - finalized the coverage counts
Added .ropeproject to gitignore
Added stats vector
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Rename sel_reads to scores_reads (reflects better the purpose of the command).  First working import; pairs and scores reads from unpaired map files, outputing a paired map file
resyncing my tree...
Code cleanup
Allow alignment scores to be output and input from map files in hex as well as decimal
Initial commit of code to calculate MAPQ fields in map2sam
Generate MQ tag if phred scores are calculated
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Add support for UQ and PQ options SAM flags