John Marshall

I wrote a brief comment as a counterpoint to similarly content-free brief comments from CMake advocates, in response to https://github.com/ebiggers/libdeflate/pull/101#issuecomment-718326339. I did not wish to derail this PR or add...

This is the same problem as arq5x/bedtools2#830 and bowtie2 itself will soon experience it too. The Conda build has just been first to use an affected compiler, and then has...

Confirmed that removing `-I .` makes compilation succeed on macOS with an affected compiler where it did not work before. As you (currently) have no _.cpp_ source files in subdirectories,...

Note that with that PR merged, _BOWTIE2_VERSION_ identifies the current version as 2.4.2, but presumably no such version has yet been released.

Re BAM, this would probably be a use case for the proposed splitting index (see samtools/hts-specs#321) that hasn't been finalised (or implemented in HTSlib / samtools).

See also 7a54ff90f3078ce9b2d2c0dce4eed8f19a9171ec, af9768db12647fa712d9dcc0c0743a49f5ef3424, deecae23ad7f862f42fc8f051a70796add1fddc3, and dde9bdbe4174728f99d1bbe7326ffd631539bef6. Sheesh. I didn't fix up _cram/*.h_ in the past so as not to diverge from the iolib versions, but that may no longer...

[`bcf_hdr_add_sample()`](https://github.com/samtools/htslib/blob/develop/vcf.c#L87-L120) aborts on certain errors, which some people misinterpret as crashing. Being a library function, it should really be returning an error code so the caller can decide what to...

Yes, we'll soon support `host_base` in [_.s3cfg_](http://s3tools.org/kb/item14.htm) and some equivalent in _.aws/config_. I'm not really keen to invent new environment variables — are there other tools using such an environment...

Probably you also have a _~/.aws/credentials_ file, which htslib reads first and so has already provided settings to be used. And this very issue is about not being able to...

@sb10: In that case, running under `strace` to see it opening and reading from _~/.s3cfg_ may be interesting…