Weird distance and internals bug

[jenzopr]

When uropa is run with the config.json:

"queries":[
		  {"feature":"gene", "distance":17, "internals":"T", "show.attributes":["gene_id", "gene_name", "gene_type"]}
          ],
"priority": "F",
"gtf": "x.gtf",
"bed": "x.bed"
}

and x.bed:

chr1	5	7	Other
chr1	8	55	L1

and x.gtf:

chr1	HAVANA	gene	1	10	.	+	.	gene_id "ENSMUSG00000102693"; gene_type "TEC"; gene_status "KNOWN"; gene_name "4933401J01Rik"; level 2; havana_gene "OTTMUSG00000049935.1";
chr1	ENSEMBL	gene	50	100	.	+	.	gene_id "ENSMUSG00000064842"; gene_type "snRNA"; gene_status "KNOWN"; gene_name "Gm26206"; level 3;
chr1	HAVANA	gene	200	300	.	-	.	gene_id "ENSMUSG00000051951"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Xkr4"; level 2; havana_gene "OTTMUSG00000026353.2";

the second peak (8 - start, 32 - center, 55 - end) is not annotated to the second gene (50 - start, 100 - end).
When the distance is allowed to be 18, the peak is annotated. It seems that in the case of overlapStart, the internals rescue does not work as intended.

[ckuenne]

i adapted the docu to the intended changes to the internals parameter: UROPA/docs_rst/config.rst

[jenzopr]

The default should be internals = 'none' to match the previous behavior.

[jenzopr]

@afust allowed values are
"center", "any", "none"

For backwards compatibility, also
"T", "True", "Y", "Yes" are allowed and will be treated as "center",
"F", "False", "N", "No" are allowed and will be treated as "none".