CLI development #28

tmaklin · 2024-10-31T12:37:35Z

Gate building CLI behind the cli feature.
Move cli code to src/cli.
Expose max_error_probability in lib.rs and CLI.

This is a breaking update:

sablast::matches now takes 4 parameters instead of 3.
sablast::map now takes 4 parameters instead of 3.
sablast::find now takes 4 parameters instead of 3.

Cargo.toml

src/format.rs

tmaklin · 2024-10-31T12:39:24Z

src/format.rs

+/// character representation of an alignment `alignment` to determine the
+/// nucleotide sequence of the alignment relative to the reference.
+///
+/// Only works with refined translations as the input (TODO verify).


A new Todo was discovered. If it is not a priority right now,consider marking it for later attention.
TODO verify).

Ignore

tmaklin · 2024-10-31T12:39:25Z

src/format.rs

+/// # Examples
+/// ## Format a refined translation
+///
+/// TODO Add test to relative_to_ref documentation.


A new Todo was discovered. If it is not a priority right now,consider marking it for later attention.
TODO Add test to relative_to_ref documentation.

Ignore

tmaklin · 2024-10-31T12:43:33Z

src/format.rs

+/// character representation of an alignment `alignment` to determine the
+/// nucleotide sequence of the alignment relative to the reference.
+///
+/// Only works with refined translations as the input (TODO verify).


A new Todo was discovered. If it is not a priority right now,consider marking it for later attention.
TODO verify).

Ignore

tmaklin · 2024-10-31T12:43:34Z

src/format.rs

+/// # Examples
+/// ## Format a refined translation
+///
+/// TODO Add test to relative_to_ref documentation.


A new Todo was discovered. If it is not a priority right now,consider marking it for later attention.
TODO Add test to relative_to_ref documentation.

Ignore

tmaklin · 2024-10-31T12:53:58Z

src/format.rs

+/// character representation of an alignment `alignment` to determine the
+/// nucleotide sequence of the alignment relative to the reference.
+///
+/// Only works with refined translations as the input (TODO verify).


A new Todo was discovered. If it is not a priority right now,consider marking it for later attention.
TODO verify).

Ignore

tmaklin · 2024-10-31T12:53:59Z

src/format.rs

+/// # Examples
+/// ## Format a refined translation
+///
+/// TODO Add test to relative_to_ref documentation.


A new Todo was discovered. If it is not a priority right now,consider marking it for later attention.
TODO Add test to relative_to_ref documentation.

Ignore

tmaklin added 19 commits October 1, 2024 22:21

Gate building the command line interface behind feature cli.

8b1adb4

Build command line interface for testing and packaging.

cefff2a

Move CLI sources to src/cli/.

b8fae88

Fix indent

fde641c

Add extra warnings.

45477b6

Document fields and default().

6931301

Remove qualifications from sbwt::SbwtIndexVariant.

89d6f82

Add qualifications to tests that broke.

49c33fb

Merge branch 'gate-cli-behind-a-feature' into dev

1f4c4bf

Fix links in docs.

148b55b

Tabs -> spaces.

c265018

Document run_lengths.

1d4fc17

Partial documentation for format.rs

9c93166

Fix indentation that broke at some point.

cf7a786

Remove hardcoded max_error_prob, add as an option.

8d55543

Tabs -> spaces

9f59cde

Add max_error_prob to CLI.

be7cef4

Less is more in documentation.

2a54855

Placeholder documentation for crate.

7b9d47b

tmaklin temporarily deployed to Comment on PRs October 31, 2024 12:37 — with GitHub Actions Inactive