daviesrob

The BAM specification says that BAM files [are wrapped in BGZF blocks](https://samtools.github.io/hts-specs/SAMv1.pdf#subsection.4.2), and BGZF [always includes a CRC checksum](https://samtools.github.io/hts-specs/SAMv1.pdf#subsection.4.1). Uncompressed BAM file is still BGZF-wrapped, the difference is that it...

Thanks for the very detailed report. As mentioned in #664, FORMAT strings are stored as a character array, of size `number_samples * length(longest_string)`. Shorter strings get padded with NUL bytes....

Unfortunately it looks like the simple solution here can overshoot the target depth quite badly if you set `depth_pos_fract = 1.0`, as in this example where the nominal depth limit...

This looks like a reasonable solution for the single-thread case. The tricky part will be what to do when `hts_log()` is called from a thread, which I'm pretty sure could...

`HTS_AUTH_LOCATION` was created for use with htsget, but it may work with GCS as long as you don't set `GCS_OAUTH_TOKEN`. The best way to test this would be to use...

Good to hear this. I'll leave a note here that we need to document this as a better way of supplying the token when using GCS.

I prefer not to break the API too much, so I'd probably go for adding a typedef and deprecating the old name. I expect the number of people who notice...

I think this looks OK in principle, although we should do something about the (not unlikely) possibility of the `hts_logger()` callback being called from a thread. I think at the...

This is a nice idea, but currently it changes the signature of `tbx_index()`, which would change both the API and ABI. Instead, you should make a `tbx_index2()` with the extra...

We have [`htell`](https://github.com/samtools/htslib/blob/ac22d4d4/htslib/hfile.h#L144) and [`bgzf_tell`](https://github.com/samtools/htslib/blob/ac22d4d4/htslib/bgzf.h#L215), but currently no combined `hts_tell`. However, the cases here are different from the general one because the interfaces consume the entire file before returning. You...