fix: Remove spliced alignments from DP calculation

[LKress]

For positions overlapped by spliced alignments, only reads that actually map to the position of interest are counted for the depth calculation.

Additionally fixed CI pipeline (finally)

[Copilot]

Pull Request Overview

This pull request addresses the calculation of read depth (DP) by excluding spliced alignments from being counted and updates the CI pipeline configurations.

• Fixes the DP calculation in pileups.py by excluding empty base strings.
• Bumps the project version and updates GitHub Actions workflows to newer versions and images.

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
vafator/pileups.py	Updated DP calculation to filter out empty bases.
vafator/init.py	Bumped version from 2.2.0 to 2.2.1.
.github/workflows/unit_tests.yml	Updated checkout and setup Python actions; removed Python 3.7 from the matrix.
.github/workflows/release.yml	Upgraded GitHub Actions versions and added pip cache purge.
.github/workflows/integration_tests.yml	Updated checkout and setup Python actions; removed Python 3.7 from the matrix.

Comments suppressed due to low confidence (2)

.github/workflows/unit_tests.yml:11

• Removing Python 3.7 from the test matrix could affect users still relying on that version; verify that the intended support policy is updated and documented accordingly.

python-version: ['3.8', '3.9', '3.10']

.github/workflows/integration_tests.yml:10

• Dropping Python 3.7 from the integration tests matrix might impact users on that version; ensure that this change is aligned with the project's supported Python versions and update any related documentation.

python-version: [ '3.8', '3.9', '3.10' ]