bam2stats - fixed counting of improper read pairs
gtf2gtf.py - removed reference to GFF.py
GTF.py - added missing import of IOTools
updated documantion - added tests for gtf2fasta
bam2bam.py and bam2stats.py - bugfixes
diff_gtfs.py - renamed to gtfs2tsv.py, added tests
setup.py - install pipelines when run locally
diff_gtf.py - added test case
pipeline_windows.py - first import
fixed conflicts