domagi - DuckDB-powered pangenome Swiss Army knife

Age	Commit message (Expand)	Author
4 days	Symlink in docbook schema from the guix shell environment.	Arun Isaac
4 days	Add docbook dependencies to manifest.	Arun Isaac
4 days	Detach output database after extract.	Arun Isaac
4 days	Order path_segment by the output coordinates, not the input.	Arun Isaac
4 days	End meson.build with a newline.	Arun Isaac
4 days	Move extract --context-steps option close to --node.	Arun Isaac
4 days	Refactor extract --path-range query into extract-path-range.sql.	Arun Isaac
4 days	Comment on extract-node-traversal.sql.	Arun Isaac
4 days	Remove leading whitespace.	Arun Isaac
4 days	Provide type and metavar for depth --bed-input.	Arun Isaac
4 days	Provide path range format in usage string.	Arun Isaac
4 days	Indicate that there is no graph traversal with --path-range.	Arun Isaac
4 days	Re-order AND clauses for readability.	Arun Isaac
4 days	Append extracted path range to path name.	Arun Isaac
5 days	Re-order extracted path_segment table for optimal access.	Arun Isaac
5 days	Install extract-node-traversal.sql.	Arun Isaac
5 days	Do not traverse graph when extracting segments in path range.	Arun Isaac
5 days	Allow grouping options into separate lists in refentries.	Arun Isaac
5 days	Move node traversal extraction query to its own file.	Arun Isaac
5 days	Traverse symmetrically in both directions with extract.	Arun Isaac
5 days	Test domagi extract on node extraction.	Arun Isaac
6 days	Only require documentation of non-hidden options.	Arun Isaac
6 days	Do not hide -S, --summarize flags.	Arun Isaac
6 days	Remove threads variable name.	Arun Isaac
6 days	Add -P, --progress flags.	Arun Isaac
10 days	Expose domagi script visible with pre-inst-env.	Arun Isaac
10 days	Build duckdb database only once in a setup fixture.	Arun Isaac
10 days	Symlink guix.scm to domagi-package.scm.	Arun Isaac
10 days	Update odgi to 0.9.4.	Arun Isaac
10 days	Initialize schema in crush subcommand.	Arun Isaac
10 days	Add chop subcommand.	Arun Isaac
10 days	When testing, canonicalize links before comparing them.	Arun Isaac
10 days	Canonicalize L line when building database.	Arun Isaac
2026-08-15	Error out if user-specified path does not exist.	Arun Isaac
2026-08-15	Add CI badges to README.	Arun Isaac
2026-08-15	Add domagi overlap --paths.	Arun Isaac
2026-08-15	Document website building instructions.	Arun Isaac
2026-08-15	When sorting a data frame by a single column, only pass in a string.	Arun Isaac
2026-08-15	Add domagi overlap.	Arun Isaac
2026-08-14	Move path_length to schema as view.	Arun Isaac
2026-08-14	Remove TODO note about synopses.	Arun Isaac
2026-08-14	Reverse complement sequences as required in FASTA.	Arun Isaac
2026-08-14	Fix paths --fasta SQL query.	Arun Isaac
2026-08-14	Test paths --fasta.	Arun Isaac
2026-08-14	Add manual to website.	Arun Isaac
2026-08-13	Add manual.	Arun Isaac
2026-08-13	Add website.	Arun Isaac
2026-08-13	Add introductory paragraph to README.	Arun Isaac
2026-08-13	Add short_help for subcommands.	Arun Isaac
2026-07-27	Make git repo a Guix channel.	Arun Isaac