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docs: find a gene's exons with bedspec and tidy the README's files and names - #2

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clintval merged 8 commits into
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docs/bedspec-intervals
Oct 27, 2026
Merged

clintval merged 8 commits into
mainfrom
docs/bedspec-intervals

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@clintval clintval commented Oct 27, 2026 •

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Adds a README section, before Development and Testing, that finds the exons of a gene among per-target coverage rows with bedspec 4.3.0 and its new bedspec.ext.captainslog.
The example is the one in bedspec's README, and it runs under sybil like every other example, since bedspec ~=4.3 joins the test group.

Also in the README:

  • Its examples run from tests/data, through a fixture in conftest.py, so paths read as a user's own files, like picard/hs.hs_metrics.
  • Every file it names ends in .txt. The Picard fixtures are renamed to match, and scripts/fixtures/make.sh gives the outputs of the Picard tools that take only a prefix the .txt extension too, so regenerated fixtures keep these names.
  • Each read stays on one line, except for the parenthesized with that opens two files.
  • The variables holding a histogram or metrics are named for what they hold: isize_metrics, isize_histogram, and insert_size_histogram, in place of isize (used for two different things) and hist.
  • The bedspec intro fits on one line.

bedspec joins typeline in the packages exempt from the one-week exclude-newer window, since both are released alongside captainslog.

uv run poe check-all passes: 1039 tests and 100% coverage.

Base automatically changed from feat/first-release to main October 27, 2026 01:15
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clintval force-pushed the docs/bedspec-intervals branch from 94269ce to f340e2d Compare October 27, 2026 01:17
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clintval force-pushed the docs/bedspec-intervals branch from f340e2d to 56e130d Compare October 27, 2026 01:39
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clintval marked this pull request as ready for review October 27, 2026 01:41
@clintval clintval changed the title docs: show reading captainslog records as intervals with bedspec docs: find a gene's exons with bedspec and fit the README in 100 columns Oct 27, 2026
@clintval clintval changed the title docs: find a gene's exons with bedspec and fit the README in 100 columns docs: find a gene's exons with bedspec and tidy the README's files and names Oct 27, 2026
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clintval merged commit 4d24c8e into main Oct 27, 2026
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clintval deleted the docs/bedspec-intervals branch October 27, 2026 01:55
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