Is there any way to get the variant's row index when using the iterator query()

[ruqianl]

Hi Brent,

I have been looking at the source code of hts-nim and hts-lib libraries and trying to find whether such information is recorded (Haven't got a solution).

To be clearer, for example, I have the following code :

for rec in ivcf.query(chrom): 
    # how to get the row index for this rec (row index correspond to the ith row in the supplied VCF file

Best regards,
Ruqian

[Brent Pedersen]

No, that's not possible in VCF without additional information. You'd need an external index (like grabix) to know the line number.

[ruqianl]

Right, thanks for the link Brent! and saved my time from digging into htslib more.