Rename bed_format options

[donaldcampbelljr]

In an effort to be more specific, we shall rename:

bed -> ucsc_bed

broadPeak -> encode_broadpeak
gappedPeak -> encode_gappedpeak
narrowPeak -> encode_narrowPeak

Additions:

• encode_rna_elements (already added)

- narrowPeak with column 5 with values greater than 1000 -> ns_narrowpeak ( which stands for non-strict narrowPeak)

[donaldcampbelljr]

Removed ns_narrowpeak as I realized that we would need a special format for all the other bed_formats as well (because they also have a score column with constraints of 0-1000) and that did not feel like the correct approach.

[donaldcampbelljr]

After today's discussion:

rename bed_format to data_format

data_format names will include:

strict (for the strictest compliance):
ucsc_bed (bed#+0)
bed_like (bed#+#>0, and NOT subject to the relaxed score below)
encode_narrowpeak
encode_broadpeak
encode_gappedpeak
encode_rna_elements

relaxed score (in the cases where column 5 is not between 0 and 1000):
bed_rs
encode_narrowpeak_rs
encode_broadpeak_rs
encode_gappedpeak_rs
encode_rna_elements_rs

[donaldcampbelljr]

This is now done via the above refactoring.