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Merged
gwct merged 2 commits into from
Oct 22, 2026
Merged

Readme updates #8

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d2e95c4
Use absolute GitHub links in README so they work on PyPI
gwct Oct 22, 2026
8280967
Merge branch 'main' of github.com:harvardinformatics/mafutils into re…
gwct Oct 22, 2026
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8 changes: 4 additions & 4 deletions README.md
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Expand Up @@ -20,7 +20,7 @@ This project was developed with significant assistance from large language model

`mafutils/lib/bgzf.py` is vendored from [Biopython](https://biopython.org/)
(BSD 3-Clause License option) rather than pulled in as a dependency — see the
notice at the top of that file and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md)
notice at the top of that file and [`THIRD_PARTY_LICENSES.md`](https://github.com/harvardinformatics/mafutils/blob/main/THIRD_PARTY_LICENSES.md)
for full attribution and license text.

## Installation
Expand Down Expand Up @@ -110,7 +110,7 @@ If you plan to use `--processes > 1` against compressed input, compress with

**No extra dependency for bgzip:** BGZF support is vendored in
`mafutils/lib/bgzf.py` rather than depending on the `biopython` package —
see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md)
see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](https://github.com/harvardinformatics/mafutils/blob/main/THIRD_PARTY_LICENSES.md)
for attribution.

## Index Integrity
Expand Down Expand Up @@ -297,7 +297,7 @@ bounding box over chunks that are separated, on both strands, or on different
scaffolds.

For background on these classes, filtering recipes, and an example of building
a per-species BED, see [docs/fetch-outputs.md](docs/fetch-outputs.md).
a per-species BED, see [docs/fetch-outputs.md](https://github.com/harvardinformatics/mafutils/blob/main/docs/fetch-outputs.md).

### `maf_fetch_summary.tsv`

Expand Down Expand Up @@ -538,4 +538,4 @@ verdict. Exit codes:
## Notes

For development setup (installing from a source checkout), running the test
suite, and internal implementation notes, see [`DEVELOPMENT.md`](DEVELOPMENT.md).
suite, and internal implementation notes, see [`DEVELOPMENT.md`](https://github.com/harvardinformatics/mafutils/blob/main/DEVELOPMENT.md).
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