Project data¶
See Prepare input files for commands that generate AGP, COOL/MCOOL, PAF, coverage, and GFA inputs.
Supported inputs¶
| Evidence | Extensions | Role | Required for editing? |
|---|---|---|---|
| Assembly | .agp, .agp.gz |
Authoritative editable layout | Yes |
| Edit history | <AGP-prefix>.history.json |
Compatible undo/redo timeline | No |
| Contact map | .cool, .mcool |
Heatmap and 3D-contact evidence | No |
| Assembly graph | .gfa, .gfa1, optional .gz |
Topology and overlap evidence | No |
| Synteny | .paf, optional .gz |
Reference/query alignment view | No |
| Coverage | .depth, .bedgraph, .bg, optional .gz |
Coverage track | No |
Individual file inputs also accept selected .txt and .txt.gz forms for AGP,
GFA, PAF, and coverage. Project-folder discovery uses the specific extensions in
the table. A history sidecar is never selected independently: C-Studio loads it
only when its prefix matches the selected AGP and its embedded canonical AGP
matches the current layout.
Project-folder discovery¶
Load project folder… scans regular files in the selected directory's top level. It does not recurse into subdirectories.
For each evidence type:
- filenames are ordered deterministically;
- one file is selected;
- other files of the same type are reported as ignored candidates.
For contact maps, an .mcool candidate is preferred over .cool; ties are
resolved by the deterministic filename ordering. Text inputs can be gzip
compressed. .cool and .mcool are HDF5 containers and must not be gzip
wrapped.
If the selected AGP is assembly.agp or assembly.agp.gz, the corresponding
history filename is assembly.history.json. An incompatible or malformed
sidecar is ignored rather than applied to a different layout.
Identifier compatibility¶
AGP component IDs provide the immutable lookup keys used to project evidence into the edited visual layout. The following identifiers should agree:
- AGP component column 6;
- contact-map chromosome/bin names;
- PAF query names;
- coverage chromosome names;
- GFA segment names.
Renaming a contig in C-Studio changes its exported display name while retaining the immutable source lookup key during the session.
Partial projects¶
C-Studio can load a folder containing only a subset of the supported types. An AGP-only project supports layout editing and AGP export. Evidence panes remain empty or disabled until their corresponding files are loaded.
Loading a new project folder replaces the current workspace. Use Clear all loaded data… to explicitly remove every source; use Reload assembly… to restore the initially loaded AGP while retaining other evidence sources.
Platform note¶
The desktop application uses Tauri's native dialog plugin for project folders and individual data files on macOS and Windows. A complete real-Windows click-through remains a separate release QA step. Browser preview can fall back to web inputs for text files, but it does not provide the desktop HDF5 backend.