Unnecessary error messages when reading in BED files

[hansenp]

When I try to read a BED file with only three columns via 'Enter BED file', I get the following error message:

That is not correct. The BED format only requires 3 columns: https://genome.ucsc.edu/FAQ/FAQformat.html#format1

Also, when I try to read a BED file with a track annotation header line, I get an error message. This is annoying and unnecessary. Such lines always start with browser or track and could therefore simply be skipped.

[pnrobinson]

The way the application is written, we are using some of the data from BED6 format in this class because we are creating a GopherGene object, GopherGene gene= new GopherGene(accession, accession, isNoncoding, chrom, strand); and so the accession is taken from the fourtyh field of BED6. It would require a major rewrite to do this in another way and so it is probably best to leave the requirement for BED6 now unless there emerges a concrete need for BED3.