Aaron Quinlan comments

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                                            Aaron Quinlan

Blank BED files throw an error

Thanks Jacob, I will look into this asap. Aaron

VCF output truncated, if blank line follows header

Thanks for reporting this Ryan. It seems odd to me that blank line would be allowed in VCF. I will have a look at this soon, but am travelling to...

support for additional VEP terms

I honestly think this is the realm of the new gemini workflow based upon vcfanno and vcf2db. Our goal is the switch over to this entirely this year.

support for additional VEP terms

If they are in the VCF via vcfanno or VEP, they make it into the database. @brentp - can you corroborate?

support for additional VEP terms

Gotcha, looks like we would need to update the logic in geneimpacts and in vcf2db to support this.

unionbedg cannot handle multiple columns

Hi there, Something must be odd on your system (are you using a shell other than BASH?), as on my OSX machine using BASH, `unionbedg` works with native gzip files...

unionbedg cannot handle multiple columns

Thanks for the update. The `unionbedg` tool assumes strict BEDGRAPH (four columns) format for its input. Changing that would require substantial refactoring. Could you do a `

unionbedg cannot handle multiple columns

Ah, I see. If you have the time and interest to explore expanding the functionality, I would be very grateful. I suspect most of the work would be expanding `PointWithDepth`...

terminate called after throwing an instance of 'std::out_of_range'

What version of bedtools? Could you see if the problem exists with the current version (2.28.0)? Could you share a minimal bam file and gtf that create this problem? Without...

Add a 'flip' tool.

Agree, but harder for BAM files. It's is certainly debatable though.