Fgpyo

What's Changed

* Offer GZIP support for `Metric` IO by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/52
* Add method `is_clipping` to `CigarOp` by kockan in https://github.com/fulcrumgenomics/fgpyo/pull/54
* Add `vcf` module by TedBrookings in https://github.com/fulcrumgenomics/fgpyo/pull/47
* Suppress stderr printing when sam indices are older than SAM file by TedBrookings in https://github.com/fulcrumgenomics/fgpyo/pull/48
* Add `Template.write_to()` by msto in https://github.com/fulcrumgenomics/fgpyo/pull/62
* Add `set_tag` method to `Template` by msto in https://github.com/fulcrumgenomics/fgpyo/pull/59
* Add header property by msto in https://github.com/fulcrumgenomics/fgpyo/pull/58
* Use rtd theme by msto in https://github.com/fulcrumgenomics/fgpyo/pull/63
* Add `chrom1`/`chrom2` arguments to `add_pair()` by msto in https://github.com/fulcrumgenomics/fgpyo/pull/61
* `fast_concat()` for `Metric` by kockan in https://github.com/fulcrumgenomics/fgpyo/pull/53
* Fix install and test by TedBrookings in https://github.com/fulcrumgenomics/fgpyo/pull/71
* Adding the option to specify the sort order of an output SAM file produced by `SamBuilder` by NatPRoach in https://github.com/fulcrumgenomics/fgpyo/pull/25
* Fix type problems found by latest mypy by TedBrookings in https://github.com/fulcrumgenomics/fgpyo/pull/75
* Have `ContigBuilder.add()` default to adding 1x the bases provided by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/76
* Add VCF module to docs and fixup docs warnings by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/78
* Add a context manager for zipping FASTX files by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/77

New Contributors

* clintval made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/52
* kockan made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/54
* TedBrookings made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/47
* msto made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/62

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.1.0...0.1.1

What's Changed
* Metric.read should support skipping extra columns by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/50. This is a breaking change!


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.0.8...0.1.0

What's Changed
* add support for unmapped BAM file reading by danielmarrama in https://github.com/fulcrumgenomics/fgpyo/pull/37
* Fix black formatting in 37 by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/38
* Update the docs for new modules by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/39
* Fixes to sam API docs by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/44

New Contributors
* danielmarrama made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/37

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.0.7...0.0.8

What's Changed
* Add `record(rec: AlignedSegment)` function to `ProgressLogger` Issue 31 by sam-white04 in https://github.com/fulcrumgenomics/fgpyo/pull/33
* Update .readthedocs.yml by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/35
* Comments should go after constants by yfarjoun in https://github.com/fulcrumgenomics/fgpyo/pull/36
* Create an Io class/module that provides some functions similar to fgbio's Io class issue 11 by sam-white04 in https://github.com/fulcrumgenomics/fgpyo/pull/30

New Contributors
* yfarjoun made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/36

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.0.6...0.0.7

What's Changed
* Reference set builder dev by sam-white04 in https://github.com/fulcrumgenomics/fgpyo/pull/24
* Remove square brackets when writing lists to disk by sam-white04 in https://github.com/fulcrumgenomics/fgpyo/pull/28
* Metric should handle Optional fields better by sam-white04 in https://github.com/fulcrumgenomics/fgpyo/pull/29
* [feat] adding column_it to fgpyo.util.string by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/34

New Contributors
* sam-white04 made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/24

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.0.5...0.0.6

What's Changed
* A bunch of re-organization followed by adding a bunch of code by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/14
* Add isort as a dev dependency and use it to keep imports tidy. by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/16
* New Template class and TemplateIterator. by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/15
* Added a function to the sam module to calculate mms, nm, etc. by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/17
* Add ability to set mapq when adding pairs and single reads to SamBuilder by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/21
* Fixed the str() method for SupplementaryAlignment to safely round-trip. by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/18
* Let the pysam requirement float. by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/23

New Contributors
* tfenne made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/14

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.0.4...0.0.5