pipeline_quickstart - add emacs autosave file exclusion
pipeline_quickstart - rename publish_report to publish
pipeline_quickstart - rename publish_report to publish
Local.py - added export_files option
bamfiles - enable stripping of sequence and quality information from bam files
bam2stats - improved paired read counting
bam2stats - fixed counting of improper read pairs
Documentation and minor changes to fasta2counts.py
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
fasta2counts - merged with fasta2table
rnaseq_bams_vs_bams.py - renamed to diff_bam.py
rnaseq_bam_vs_exons.py - renamed to bam_vs_gtf.py