A simple tool to quickly (!) tell you about the final-ish alignment present in a BAM file at runtime. This is useful for monitoring progress as a large, position-sorted BAM file is being generated. Since BAM files are compressed, tail is not useful for this! bamtail runs on python3.
$ bamtail sample1.bam
chr4:34062067
$ bamtail sample2.bam sample3.bam sample4.bam
sample2.bam: chr3:23469490
sample3.bam: unmapped
sample4.bam: chr14:1045735
You can install with pip3:
pip3 install https://github.com/abjonnes/bamtail/tarball/master
Or, with setuptools installed:
git clone https://github.com/abjonnes/bamtail.git
cd bamtail
python3 setup.py install