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

[msto]

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 in #124 , and also simplified the typing on io.to_reader() and io.to_writer() (per Clint's suggestion)

---

note I want to keep this separate from the MetricWriter feature branch, but it's dependent on the Metric._read_header method introduced in that branch.

I am waiting to merge until #123 is merged.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 89.74%. Comparing base (318ff98) to head (7b21816). Report is 12 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #103      +/-   ##
==========================================
+ Coverage   89.71%   89.74%   +0.02%     
==========================================
  Files          18       18              
  Lines        2207     2213       +6     
  Branches      489      491       +2     
==========================================
+ Hits         1980     1986       +6     
  Misses        149      149              
  Partials       78       78              

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[msto]

That's fair.

I would be open to refactoring so .read() remains specific to Metric-formatted files. In that case I'd suggest providing a .read_picard() method or similar, which would filter comment lines before calling .read() under the hood.

I do think it would be generally valuable to have built-in support for reading Picard metrics into a Metric, and it would be very specifically helpful for one of my clients.

[msto]

@nh13 thoughts?

[nh13]

@msto I'd like to review this one before it gets merged

[msto]

note I want to keep this separate from the MetricWriter feature branch, but it's dependent on the Metric._read_header method introduced in that branch.

I am waiting to merge until #123 is merged.

[coderabbitai[bot]]

Walkthrough

The changes in this pull request involve enhancements to the Metric class located in fgpyo/util/metric.py, specifically targeting the read method. The method's signature has been modified to include a new parameter, comment_prefix, which allows users to specify a string to identify comment lines in metric files. This enhancement enables the method to ignore lines that begin with the specified prefix during the parsing of the file header.

The implementation of the read method has been updated to use a new helper method, _read_header, which also accepts the comment_prefix parameter. This method is responsible for reading the header while skipping empty lines or those starting with the comment prefix. If no valid header is found, a ValueError is raised. Additionally, the logic for checking missing fields has been adjusted to utilize a new fieldnames variable derived from the header. The error messages for discrepancies in expected and actual fields have been updated accordingly.

In parallel, a new test function, test_read_validates_no_header, has been added to tests/fgpyo/util/test_metric.py to verify the behavior of the Metric.read method when the input file lacks a header. This function tests various scenarios, ensuring that appropriate exceptions are raised when the header is absent.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Metric
    participant File

    User->>Metric: call read(path, ignore_extra_fields, comment_prefix)
    Metric->>File: open(path)
    File-->>Metric: read lines
    Metric->>Metric: _read_header(lines, comment_prefix)
    Metric->>Metric: skip empty/comment lines
    Metric->>Metric: validate header
    alt No valid header found
        Metric-->>User: raise ValueError("No header found.")
    else Valid header found
        Metric->>Metric: process fields
        Metric-->>User: return metrics
    end

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