0.1.1

What's Changed

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

New Contributors

• @clintval made their first contribution in #52
• @kockan made their first contribution in #54
• @TedBrookings made their first contribution in #47
• @msto made their first contribution in #62

Full Changelog: 0.1.0...0.1.1

0.1.0

What's Changed

• Metric.read should support skipping extra columns by @nh13 in #50. This is a breaking change!

Full Changelog: 0.0.8...0.1.0

0.0.8

What's Changed

• add support for unmapped BAM file reading by @danielmarrama in #37
• Fix black formatting in #37 by @nh13 in #38
• Update the docs for new modules by @nh13 in #39
• Fixes to sam API docs by @nh13 in #44

New Contributors

• @danielmarrama made their first contribution in #37

Full Changelog: 0.0.7...0.0.8

0.0.7

What's Changed

• Add record(rec: AlignedSegment) function to ProgressLogger Issue #31 by @sam-white04 in #33
• Update .readthedocs.yml by @nh13 in #35
• Comments should go after constants by @yfarjoun in #36
• Create an Io class/module that provides some functions similar to fgbio's Io class issue #11 by @sam-white04 in #30

New Contributors

• @yfarjoun made their first contribution in #36

Full Changelog: 0.0.6...0.0.7

0.0.6

What's Changed

• Reference set builder dev by @sam-white04 in #24
• Remove square brackets when writing lists to disk by @sam-white04 in #28
• Metric should handle Optional fields better by @sam-white04 in #29
• [feat] adding column_it to fgpyo.util.string by @nh13 in #34

New Contributors

• @sam-white04 made their first contribution in #24

Full Changelog: 0.0.5...0.0.6

0.0.5

What's Changed

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

New Contributors

• @tfenne made their first contribution in #14

Full Changelog: 0.0.4...0.0.5

0.0.4

What's Changed

• Fix README links to the main branch by @nh13 in #6
• Add classes for representing read structures by @nh13 in #7

Full Changelog: 0.0.3...0.0.4

Release 0.0.3

This is a minor release of fgpyo.

Bugfixes:

Various Metric class bugfixes:

• fixed issue with parsing Optional types on attr classes
• fixed issue with imports / naming that was being ignored due to error handling
• fixed issue with partial functions not being called correctly

Features:

• improved error handling by adding custom error class

Release 0.0.2

This is a minor release of fgpyo to loosen the python version requirement from >=py3.6.10 to >=3.6.0 (#1)

Release 0.0.1

This is the first release of fgpyo version 0.0.1.

Modules included are:

• fgpyo.sam.SupplementaryAlignment: stores a supplementary alignment record produced by BWA and stored in the SA SAM tag
• fgypo.sam.Metric: a class for all metric-like tab-delimited files. Metric files are tab-delimited, contain a header, and zero or more rows for metric values. This makes it easy for them to be read in languages like R. This allows implementing classes to extend attr classes, have attributes be typed, and read and write to tab-delimited files with types properly preserved. This is inspired from the Metric in the fgbio-scala repository.
• ancillary methods to support inspecting and maintaining types in fgypo.sam.Metric