-R output is truncated

[dwaggott]

I seem to be getting truncated output using -R and not -T when running isec. I can't narrow down what's going on. The files below were about as small and reproducible as I could get.

#  3 unique records using -R
bcftools-dev isec -O z -n =1 -w 1 tmp1.vcf.gz tmp2.vcf.gz -R tmp3.bed.gz > tmp4.vcf

# lots of records using -T
bcftools-dev isec -O z -n =1 -w 1 tmp1.vcf.gz tmp2.vcf.gz -T tmp3.bed.gz > tmp4.vcf

tmp1.vcf
tmp2.vcf
tmp3.bed

[pd3]

A duplicate of #562 perhaps?

[dwaggott]

Don't think so. Ive seen that before. The discrepancy didn't happen with view but I'll double check.

…

On Wed, May 24, 2017 at 10:35 PM pd3 ***@***.***> wrote: A duplicate of #562 <#562> perhaps? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#619 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADAQeLqKHMWUF73zrFG-sdgsX4a1cnf9ks5r9RMGgaJpZM4NkOmv> .

[pd3]

I verified that this is a real problem, related but not duplicate of #562. Again the bed file contains overlapping intervals which the -T has problems with. This should be fixed in the next release of bcftools and htslib.