Bamaligncleaner

Add fasta ref filtering

**Full Changelog**: https://github.com/maxibor/bamAlignCleaner/compare/0.3...0.4

What's Changed
* Add filtering from user provided reference list by maxibor in https://github.com/maxibor/bamAlignCleaner/pull/6

**Full Changelog**: https://github.com/maxibor/bamAlignCleaner/compare/0.2.2...0.3

Same as 0.2.1, new release to get Zenodo DOI

- Solve issues 1 2 3

Changelog
* Add solution to PySam header check [826](https://github.com/pysam-developers/pysam/issues/826)
* Better logging
* Default output to STDOUT
* Add automatic indexing for non-index files

Initial release