Cnv-from-bam

Headlines
Small change - can now choose to filter out or include supplementary mappings.

**Full Changelog**: https://github.com/Adoni5/cnv_from_bam/compare/v0.4.0...v0.4.1

Headline
* Remove `PyO3-log` for maximum speed. This means that log messages will not be handled by python loggers. Can set log level on call to `iterate_bam_file`
* This fixes a regression in v0.3

What's Changed
* Remove PyO3 log, impment rust side log level filtering by Adoni5 in https://github.com/Adoni5/cnv_from_bam/pull/10


**Full Changelog**: https://github.com/Adoni5/cnv_from_bam/compare/v0.0.3...v0.4.0

Highlights
We have added suppression of output by using `PyO3-log` to filter log messages on the python side
Disable the progress bar for BAM iteration by setting the `CI` env variable.

What's Changed
* Feature/python logging by Adoni5 in https://github.com/Adoni5/cnv_from_bam/pull/8


**Full Changelog**: https://github.com/Adoni5/cnv_from_bam/compare/v0.0.2...v0.0.3

Highlights
1. Reimplemented in pure rust for BAM parsing (using Noodles, thanks (zaeleus)[https://github.com/zaeleus]!).
2. Uses a much more sensible number for threading if not provided.
3. Allows iteration of BAMs in a directory
4. Adds pre-commit
5. Allows the use of either `BAI` or `CSI` indexes, or indexless BAMs.
6. Improved progress bars

What's Changed
* Rewrite in pure rust using noodles by Adoni5 in https://github.com/Adoni5/cnv_from_bam/pull/1
* Issue2/add-pre-commit by Adoni5 in https://github.com/Adoni5/cnv_from_bam/pull/5
* Fix the readme by Adoni5 in https://github.com/Adoni5/cnv_from_bam/pull/6
* Issue4/read bams from directory by Adoni5 in https://github.com/Adoni5/cnv_from_bam/pull/7

New Contributors
* Adoni5 made their first contribution in https://github.com/Adoni5/cnv_from_bam/pull/1

**Full Changelog**: https://github.com/Adoni5/cnv_from_bam/compare/v0.0.1...v0.0.2

Initial working release - no support on `linux aarch64`, uses `rust-htslib`.

**Full Changelog**: https://github.com/Adoni5/cnv_from_bam/commits/v0.0.1