daviesrob

I've had mixed results with this. For an uncompressed input file with no B-type tags, this PR is about 10% slower on an old Sandy Bridge-era CPU compared to develop....

Yes, it would still be useful, thanks. As James mentioned, [`bam_construct_seq`](https://github.com/samtools/htslib/blob/8016127/cram/cram_samtools.c#L45) could be used as a starting point, although you'd probably want to pass in a `bam1_t` pointer directly and...

I'd say alternative 1, on the grounds that you're most likely to want to set everything - although you'd probably want to include a pointer to the `bam1_t` struct to...

Yes, I think it's roughly the right direction. I'd use a single pointer to the `bam1_t` struct. The double one is likely a relic of the [ancestor of `bam_construct_seq` in...

@jblachly Good spot. Yes, it should return -2 when `bcf_record_check()` fails. I will adjust it so that it behaves as intended.

Commit 9845bc9 makes `bcf_record_check()` return -2 on error, so problems should now be more obvious.

Thanks for the comprehensive report. It looks like this is the problem with your copies of gcc: ``` gcc: fatal error: -fuse-linker-plugin, but liblto_plugin.so not found ``` which I suspect...

There's something a bit odd about your set-up, as `./configure` with no `--prefix` would normally try to install in `/usr/local/`. Or did you run `./configure` again with `--prefix`? Anyway, it...

This is certainly worth looking into, especially as most users should now be on Linux distributions that include zstd packages. We'll need to think carefully about exactly how we integrate...

Is the problem caused by trying to do lots of index look-ups, or by having a very long delay between generating the credentials and actually trying to open the file?...