Handling gzipped file names correctly now. Also adding in a helper f…

[zrm22]

…unction to build kmers for later use.

Description

Simple change so that the read mapping file has the correct name when the fastqs are gzipped.

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

• [x] CHANGE (fix or feature that would cause existing functionality to not work as expected)
• [ ] FEATURE (non-breaking change which adds functionality)
• [ ] BUGFIX (non-breaking change which fixes an issue)
• [ ] ENHANCEMENT (non-breaking change which improves existing functionality)
• [ ] NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have updated relevant documentation

Changelog entry

Please add a one-line changelog entry below. This will be copied to the changelog file during the release process.

Simple change so that the read mapping file has the correct name when the fastqs are gzipped.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 7.69231% with 12 lines in your changes missing coverage. Please review.

Project coverage is 82.80%. Comparing base (03b7fb1) to head (2dbaed2). Report is 38 commits behind head on main.

Files	Patch %	Lines
.../net/maizegenetics/phgv2/pathing/AlignmentUtils.kt	7.69%	11 Missing and 1 partial :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #206 +/- ## ========================================== - Coverage 82.99% 82.80% -0.20% ========================================== Files 77 77 Lines 5041 5053 +12 Branches 834 837 +3 ========================================== Hits 4184 4184 - Misses 546 557 +11 - Partials 311 312 +1 ```

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