[ENH] Support for hg19 style chromosome names

[J-Bradlee]

As part as the feature implementations for version 1.1. See #27

Provide support for hg19 style chromosome names in the input bam files

• [x] For v37 reference genome

[J-Bradlee]

Update:

Its seems that the wrong chromosome nomenclature can be used, specifically during the cnvnator and lumpy steps, affecting the other perl scripts.

I am going to create a new feature which checks the input bam files to make sure they have the right naming convention. If they do not like for hg19 and grch37, they can provide an option to continue with the correct naming convention. To extend this further I think its best to check that all the input bams have the same naming convention.

[J-Bradlee]

Note simply add the -hg19 flag like so:

docker run -v $refdata_path:/app/ref-data   -v $project_folder:/app/project_folder   -v $input_path:/app/input   /app/clinsv/bin/clinsv -r all -p /app/project_folder/ -i "/app/input/*.bam" -hg19 -ref /app/ref-data/refdata-b37 &

To use with hg19 nomenclature. Note this only works with grch37 as reference genome.