BED file with a space delimiter misses the first annotation

[gaitat]

I have these two bed files:

BED file with a space delimiter

chr2 0 1
chr2 2 3
chr2 4 5
chr2 6 7
chr2 8 9

BED file with a tab delimiter

chr2	0	1
chr2	2	3
chr2	4	5
chr2	6	7
chr2	8	9

I load them into igv with:

            tracks: [
                {
                    name: "spaces",
                    type: "annotation",
                    format: "bed",
                    indexed: false,
                    // delimiter: ' ',
                    url: "http://127.0.0.1:8081//examples/annotation_edge_data_with_spaces.bed",
                },
                {
                    name: "tabs",
                    type: "annotation",
                    format: "bed",
                    indexed: false,
                    // delimiter: '\t',
                    url: "http://127.0.0.1:8081//examples/annotation_edge_data_with_tabs.bed",
                },
            ]

but the first annotation of the bed file with spaces does not show up. (I use a locus: "chr2:1-20")

It doesn't seem that specifying the delimiter key makes a difference.
Even If I add 100 to the genomic location, I dont see a difference. The first annotation in the bed file with spaces does not get drawn.

[jrobinso]

Thanks for the report. Its not specified at UCSC, but the general consensus seems to be that bed files should be tab delimited. For sure a space delimited bed file will not work with many tools. Having said that, as its not specified we have tried to be whitespace agnostic, and I will fix this.

[jrobinso]

See, for example https://bedtools.readthedocs.io/en/latest/

[gaitat]

Maybe this is helpful. Just observed that when I add a line with # on top of the BED file with a space delimiter, then it works fine. i.e.

#
chr2 0 1
chr2 2 3
chr2 4 5
chr2 6 7
chr2 8 9

[jrobinso]

Yes I see the issue, it a little bit tricky to fix but I will get to it in asap, there is a point release already tested and it won't make that one. In the meantime a leading header line will work as you discovered. Or just make the files tab delimited. Most tools that accept bed files are going to assume tab delimitation, bedtools requires it for example.

[gaitat]

Thanks