samtools/htslib — pull request #113 by mcshane (2014-07-10 20:36:42+00:00)
Title: hts_file_type: correct return of FT_VCF_GZ

Actually I have 3 question about this function:

1. Can we remove the bits about detecting based on filetype extension? `.bcf` returns `FT_BCF_GZ` at the moment, but what if the file is uncompressed BCF? I noticed in a few recent issues that some are using the `.bcf.gz` convention for compressed and `.bcf` for uncompressed. Removing this detection should work with the cases I see in the codebase. Is performance the reason for having this in the first place?

2. This is called `hts_file_type`, but is specific to VCF/BCF. Should it be in vcf.c/vcf.h and renamed `bcf_file_type`? Or is the intention that we could add in SAM/BAM/CRAM to this too?

3. Is there a way to check that the compression was with bgzip rather than gzip?