Allow user to customize chromosome label in probe query script

[ggirelli]

Is your feature request related to a problem? Please describe.
The query script(s) require to specify a region in the chrN:XXX,YYY format, which forces the user to label chromosomes (or fragments) with the "chr" prefix, which can be useless in certain scenarios.

Describe the solution you'd like
Add a new script argument where the regular expression can be defined by the user.

[ggirelli]

Also remove the prefix 'chr' from the default regular expression parsing the region string.

[ggirelli]

Or, even better, replace the input string to be parsed with three separate input arguments: feature, start and end. This would solve many issues due to parsing and remove the requirement for regexp knowledge from the user.

[ggirelli]

Implemented the following in v2.0.4 (soon to be released).

Both probe and probe set query scripts have two arguments instead of the previous region:

• a mandatory "chrom" argument, which is not strictly a chromosome, but any feature in the database
• a facultative "--region" argument that accepts a start-end string.

When the --region argument is not used, the whole feature is queried.

Also, note that when the --region argument is not used, the feature size is obtained by querying a DAS server. To use the size based on the database oligos use the --no-net option.

[ggirelli]

Switched from

a facultative "--region" argument that accepts a start-end string.
to a facultative --region argument that accepts two space-separated int values: start and end respectively. If start and end coincide, the effect is the same as when --region is omitted.