Thanks for reporting this issue and workaround Ulf. I've committed a fix that addresses this issue by only includeing the -split option for BED/GFF/GTF datasets and not VCF:
https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed872e58b4691643...
Best, J.
On Sep 12, 2013, at 6:45 AM, Ulf Schaefer wrote:
Dear Jeremy
Thank you for your reply and sorry for not being clear. In short I solved the problem. Below is some info, in case this is useful for someone else.
Thanks for your help
The situation was:
On Main: Visualisation of the SAM/BAM file -> OK Visualisation of the VCF file -> OK
On my local install: Visualisation of the SAM/BAM file -> OK Visualisation of the VCF file -> FAIL
The reason is that this command fails:
grep -v '^#' /data/database/files/000/dataset_596.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -g /data/database/files/000/dataset_598.dat > temp.bg ; bedGraphToBigWig temp.bg /data/database/files/000/dataset_598.dat /data/database/files/000/dataset_609.dat
with "Input error: found interval with block-counts not matching starts/sizes"
Where dataset_596.dat is my vcf and /data/database/files/000/dataset_598.dat is my genome file.
This is produced by the bedtools genomecov bit of the command, which appears to have some sort of problem with the vcf input in combination with the -split option. The problem disappears with the installation of the latest version of bedtools (v2.17.0), but if you are using the version that you get from yum (v2.15.0) you run into this error.
Ulf
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