Hey folks, awesome tool!

It seems the app executes any javascript that might be found inside a BED file. For example, using the following BED file launches an alert box:

chr2<script>alert('hello!')</script>	789	1020

I don't think it's a security issue since the data is local/there's no auth in your app, so feel free to close, but just FYI :)

To support other species, we will need to provide other species genome builds (chrom and length files) on the interface, but also want to allow the user to upload their own for generality.

The UCSC files that bedqc uses internally use the "chr1" convention. User files may not.

this would be based on the initial QC specs matching the spec. would need to re-read the user file and update the delimiter and newline accordingly.

a scrollable text field would be nice here.

A nice feature would be to plot interval densities along each chromosome with something like ideogram.js (https://www.biostars.org/p/305698/)

for instance, it would nice to know the percentage of query intervals per chromosome that overlapped the target -- in addition to raw counts.

need to update references and bedtools intersect command

the ability to add slop, subtract, complement from a user's current interval set should be made available when performing qc. maybe only the previous command should have the ability to download (related to #15).

output section illustrates how the file has been updated to provide provenance.

Also, possibly to fail gracefully with informative error when input file is too big?

I think this is a neat tool and was just trying it out today. I am curious about one potential issue. I've noticed if the first 3 fields are separated by tab but any subsequent fields are separated by another delimiter (e.g. space) then bedqc will give green checks all around but incorrectly identify the file as having 3 fields. Files where the first 4 fields are delimited by tabs but with space delimitation afterwards seem to run through bedtools intersect (and I assume other functions) fine so this may rarely be an issue but I assume inconsistent delimitation of this type may happen often (like appending extra columns to a bed file) and it may help for bedqc to explicitly report something like this. I apologize if I'm simply missing something though or if this is a trivial point.

This would be very helpful for the first report to detect unexpected interval length profiles. The plot is also helpful, but quick interpretation can be distorted from large outliers

Beyond intersection with Gaps, intervals beyond the chrom end and intervals on contigs that belong to only one genome build are other important indicators.

When intersecting refseq in GRCh37 with the Ensembl whole gene track, here is what I get (1 hit on chr1)

Columns 9, 11, and 12 can and typically do have commas.
https://bedtools.readthedocs.io/en/latest/content/general-usage.html