Matt Stone

This PR includes two minor QoL fixes - I found the aliased import of `DataclassInstance` to `DataclassesProtocol` unnecessary, especially since it conflicted with the naming convention of `AttrInstance` - I...

feat: Add MetricWriter class

1

Closes #88. I've adapted the `DataclassWriter` from https://github.com/msto/dataclass_io/ to work with Metrics.

feat: Support reading Picard-style metrics files with comments above the header

5

It would be helpful if `Metric.read` could parse metrics files with comments above the header, such as those produced by Picard. I've updated `Metric.read` to use the `read_header()` method introduced...

It would be great to have a utility function to extract a UMI from a read name, similar to the functionality provided by `fgbio CopyUmiFromReadName` http://fulcrumgenomics.github.io/fgbio/tools/latest/CopyUmiFromReadName.html

Could be helpful to have Hamming and Levenshtein distance available

It'd be convenient to have a method that exposes the built FASTA as a `pysam.FastaFile` , e.g. to condense the following ```py fasta_path = tmp_path / "foo.fa" fasta_builder.to_file(fasta_path) fasta_file =...

`Metric` only supports tab-delimited input and output. Supporting comma-delimited files should account for the custom parsing of `list` and other comma-delimited fields. One possible solution could be to use `csv.DictReader`...

There is currently nothing preventing the user from defining an undecorated subclass of `Metric`

Consider renaming the `types`, `inspect`, `logging`, and `string` modules to avoid shadowing stdlib

Metric wishlist

4

Hey @nh13 @tfenne , I'd like to consolidate a wishlist of features/improvements to the `Metric` class. Their absence has blocked the use of `Metric` in client contexts (of note, #103...