vcfanno is slient when the tabix index is older than the bed/vcf file

[zzupmc]

Hi,

thanks for this excellent tool. I noticed that when the index file is older than the annotation file, the annotated vcf file has header information, but the variant line has no expected annotations.

##INFO=<ID=ClinPred_Score,Number=1,Type=Float,Description="calculated by max of overlapping values in column 6 from /home/pmi/share/genomes/Hsapiens/GRCh37/variation/clinpred.bed.gz">

vcfanno is silent in this situation.

vcfanno version 0.3.1 [built with go1.11]

If you have encountered an error, please include:

• [ ] minimal conf and lua files that you are using.

[[annotation]] file="/home/pmi/share/genomes/Hsapiens/GRCh37/variation/clinpred.bed.gz" names = ["ClinPred_Score"] columns = [6] ops = ["max"]

• [ ] urls or actual files for annotations in conf file. https://sites.google.com/site/clinpred/products-services

• [ ] minimal query file.

• [ ] the command you used to invoke vcfanno /home/pmi/share/anaconda/bin/vcfanno -p 4 test.conf test.vcf.gz |bgzip -c >test.anno.vcf.gz

• [ ] the full error message

vcfanno produces no error message

[brentp]

I have pushed a fix for this--it now outputs a warning if the index has been modified more recently than the data file--to an upstream dependency. thanks for reporting.