Full documentation is available at http://contra-cnv.sourceforge.net.
Included NDE and WGCNV workflows.
Removed FASTA dependency. Removed VCF support. Removed PDF file.
Updated online documentation.
Added option to remove Duplicates
Fixed a bug with "chr" named chromosomes in cn_apply_threshold
Catch errors with bam files do not contain reads in a targeted chromosome.
Fixed baseline.py scalability to large sample size
Now compatable with R2.14+