about summary refs log tree commit diff
AgeCommit message (Collapse)Author
4 daysEnd meson.build with a newline.Arun Isaac
4 daysMove extract --context-steps option close to --node.Arun Isaac
4 daysRefactor extract --path-range query into extract-path-range.sql.Arun Isaac
4 daysComment on extract-node-traversal.sql.Arun Isaac
4 daysRemove leading whitespace.Arun Isaac
4 daysProvide type and metavar for depth --bed-input.Arun Isaac
We also fix the test to pass in a string rather than a Path.
4 daysProvide path range format in usage string.Arun Isaac
4 daysIndicate that there is no graph traversal with --path-range.Arun Isaac
5 daysRe-order AND clauses for readability.Arun Isaac
It's nice to have the $1, $2 and $3 line up in that order.
5 daysAppend extracted path range to path name.Arun Isaac
5 daysRe-order extracted path_segment table for optimal access.Arun Isaac
5 daysInstall extract-node-traversal.sql.Arun Isaac
5 daysDo not traverse graph when extracting segments in path range.Arun Isaac
5 daysAllow grouping options into separate lists in refentries.Arun Isaac
5 daysMove node traversal extraction query to its own file.Arun Isaac
5 daysTraverse symmetrically in both directions with extract.Arun Isaac
5 daysTest domagi extract on node extraction.Arun Isaac
6 daysOnly require documentation of non-hidden options.Arun Isaac
6 daysDo not hide -S, --summarize flags.Arun Isaac
6 daysRemove threads variable name.Arun Isaac
The threads variable name can be derived automatically from the --threads option name.
6 daysAdd -P, --progress flags.Arun Isaac
10 daysExpose domagi script visible with pre-inst-env.Arun Isaac
This eases testing of domagi during development.
10 daysBuild duckdb database only once in a setup fixture.Arun Isaac
10 daysSymlink guix.scm to domagi-package.scm.Arun Isaac
10 daysUpdate odgi to 0.9.4.Arun Isaac
10 daysInitialize schema in crush subcommand.Arun Isaac
We need to initialize the schema in the output database so that we get things like views.
10 daysAdd chop subcommand.Arun Isaac
10 daysWhen testing, canonicalize links before comparing them.Arun Isaac
10 daysCanonicalize L line when building database.Arun Isaac
2026-08-15Error out if user-specified path does not exist.Arun Isaac
2026-08-15Add CI badges to README.Arun Isaac
2026-08-15Add domagi overlap --paths.Arun Isaac
2026-08-15Document website building instructions.Arun Isaac
2026-08-15When sorting a data frame by a single column, only pass in a string.Arun Isaac
2026-08-15Add domagi overlap.Arun Isaac
2026-08-14Move path_length to schema as view.Arun Isaac
2026-08-14Remove TODO note about synopses.Arun Isaac
This was completed in 185b459cc11a2e8661817f2750d98f9051541761.
2026-08-14Reverse complement sequences as required in FASTA.Arun Isaac
2026-08-14Fix paths --fasta SQL query.Arun Isaac
The SQL query was completely wrong. It was most likely meant to work with an earlier version of the schema.
2026-08-14Test paths --fasta.Arun Isaac
2026-08-14Add manual to website.Arun Isaac
2026-08-13Add manual.Arun Isaac
2026-08-13Add website.Arun Isaac
2026-08-13Add introductory paragraph to README.Arun Isaac
2026-08-13Add short_help for subcommands.Arun Isaac
2026-07-27Make git repo a Guix channel.Arun Isaac
2026-07-27Add hacking instructions.Arun Isaac
2026-07-27Initial commitArun Isaac