fastenloc reads bgzipped inputs incorrectly

[probalica19]

Dear William,

I noticed hat if the provided input is compressed using bgzip (rather than gzip), fastENLOC will read all of its contents except the last line without reporting any error. Is this expected behavior?

As stated in the bgzip manual, bgzip is compatible with gzip, however going through fastenloc code I figured that the library used to decompress files is boost::iostreams::gzip_decompressor(), and in htslib github I found this issue which may be related to the issue I am experiencing with fastENLOC. Since bgzip is at least in my experience very often used especially with vcf files, it could be useful mentioning this in fastenloc documentation.

I am looking forward to hearing your thoughts on this. Thanks in advance!

Best,

probalica19

[probalica19]

Hi William,

I'd also like to add to my previous meesage that GTEx v8 eQTL annotations that are provided on this github page also seem to be bgzipped. When I run fastENLOC with those files, and then rerun with annotations that I have decompressed and then compressed again with gzip, I get the snp-level output that differs in a single snp, which also appears to be the snp in the last line of the eQTL annotation file provided.

Best,

probalica