Improve "cannot setRegion" error message / failure mode

[ryan-williams]

I am running vg and getting this error:

$ ./vg construct -r hg19.fasta -v NA12878.vcf
cannot setRegion on a non-tabix indexed file

1. help debugging would be appreciated
2. a more descriptive error message would be helpful here.

I see that it comes from vcflib but that's all I've got.

[ekg]

tabix is in htslib. You use it to
index "block gzipped" (bgzipped) files.

You use bgzip and tabix like this:

bgzip NA12878.vcf
tabix -p vcf NA12878.vcf.gz

Now you can use the VCF file for construction:

./vg construct -r hg19.fasta -v NA12878.vcf.gz

Probably the error message (and you're right that it's in vcflib) just
needs to indicate this process.

On Wed, Mar 11, 2015 at 12:04 AM, Ryan Williams notifications@github.com
wrote:

I am running vg and getting this error:

$ ./vg construct -r hg19.fasta -v NA12878.vcf
cannot setRegion on a non-tabix indexed file

1. help debugging would be appreciated
2. a more descriptive error message would be helpful here.

I see that it comes from vcflib
https://github.com/ekg/vcflib/blob/b1dfd7a73140f9b12cb8fd2a554d70188ff05cca/src/Variant.cpp#L1313
but that's all I've got.

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#6.

[ekg]

Sorry if this is pedantic, but in case someone else gets caught by it
before the fix propagates to various repos that depend on vcflib.

On Wed, Mar 11, 2015 at 12:16 AM, Erik Garrison erik.garrison@gmail.com
wrote:

tabix is in htslib. You use it to
index "block gzipped" (bgzipped) files.

You use bgzip and tabix like this:

bgzip NA12878.vcf
tabix -p vcf NA12878.vcf.gz

Now you can use the VCF file for construction:

./vg construct -r hg19.fasta -v NA12878.vcf.gz

Probably the error message (and you're right that it's in vcflib) just
needs to indicate this process.

On Wed, Mar 11, 2015 at 12:04 AM, Ryan Williams notifications@github.com
wrote:

I am running vg and getting this error:

$ ./vg construct -r hg19.fasta -v NA12878.vcf
cannot setRegion on a non-tabix indexed file

1. help debugging would be appreciated
2. a more descriptive error message would be helpful here.

I see that it comes from vcflib
https://github.com/ekg/vcflib/blob/b1dfd7a73140f9b12cb8fd2a554d70188ff05cca/src/Variant.cpp#L1313
but that's all I've got.

—
Reply to this email directly or view it on GitHub
#6.

[ryan-williams]

no that is perfect, thanks