Added simple `bin/tree-info.py` script to print information about tip names and internal node labels and edge lengths in a phylogenetic tree.
5.0.18
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.