Add explicit output format to samtools sort command in `dark/bowtie2.py`.
5.0.17
More messing with indexing BAM files.
5.0.16
Check if the SAM file in `dark/bowtie2.py` is empty by reading it and looking for a non-header line. Undo the change of `5.0.15`. Added typing hints to `dark/bowtie2.py`.
5.0.15
Always make BAM in `run-bowtie2.py`. Sigh.
5.0.14
Check whether a BAM/SAM file is empty in `run-bowtie2.py` in order to avoid calling `gatk` to mark duplicates on a file with no mapped or unmapped reads, since instead of just exiting gracefully, `gatk` crashes with the typical Java runtime stack.
5.0.13
Added `bin/add-support-to-iqtree2-issue-343.py` script for adding support labels to nodes in trees produced by `iqtree2` when (if not run with `-keep-ident`) it adds nodes and tips for identical sequences. `iqtree2` currently does not put a support label on (the edge leading to) the tip in the original processing or onto the nodes introduced by adding tips for the identical sequences. This is described in the `iqtree2` GitHub [issue 343](https://github.com/iqtree/iqtree2/issues/343).