John Marshall

It goes alongside the other flag options **on the commands that are doing linking**. All those _*.o_ recipes should not include `$(LDFLAGS)`; having it there will lead to “argument unused...

For macOS users, the one critical item that needs to be listed on a roadmap is Bioconda support for native `osx-arm64`. (See also #23454, #35579, #36300, bioconda/bioconda-utils#706, #41702, #45948, and...

99999999999999999999 is larger than 264. It shouldn't really crash (I haven't reproduced that yet), but it's also not something you should expect to work and is not very useful as...

The `malloc(): memory corruption` crash turns out to be a memory corruption buglet in `tview` when given enormous positions, introduced in samtools 1.10. As a memory corruption bug, it presents...

(Still waiting for conda-forge, per the conversation on bioconda/bioconda-utils#878.)

In the absence of anyone else doing anything about this, here is a first pass at the infrastructure PR that is the first step towards building packages for Python 3.11:...

Snakemake is a noarch package for which conda builds [one package file that works on all Python versions](https://anaconda.org/bioconda/snakemake-minimal/files?version=8.1.0) that meet snakemake's declared requirements. This problem affects packages for which separate...

The same is required for pysam as for any other affected package. It requires the core cabal to prioritise this work, or at least to deploy bioconda/bioconda-utils#938 and allow maintainers...

What version of samtools is it that you are running?

My theory BTW was that the OP was running a prehistoric 0.1.x version of samtools, in which `sort -o` meant “write to standard output” and `SRR23948463.bam` was being interpreted as...