@jbrowse/bandage-core 11.7.3 → 11.9.0

package/README.md

@@ -43,7 +43,7 @@ npm install @jbrowse/bandage-core
   backbone lies on. `featuresOnBackbone` renames that assembly's genes onto the
   backbone's refNames, and `genePins` pins only those
 
-## Figures and the coarse tier
+## Figures
 
 - `figureSvg` draws a graph and its lifted walks to a standalone SVG. The
   `bandage-figure` CLI makes one from a JSON spec with no browser:
@@ -52,9 +52,43 @@ npm install @jbrowse/bandage-core
 - `figureData` returns what `figureSvg` would draw as columnar tables, for
   another graphics system to draw;
   [ggbandage](https://github.com/GMOD/ggbandage) draws them in ggplot2
-- The `bandage-fold` CLI folds every variant under a size into the reference, so
-  a graph track can draw a whole chromosome. See
-  [docs/coarse-tier.md](docs/coarse-tier.md)
+
+## Coarse tier: `bandage-fold`
+
+`bandage-fold` writes an rGFA with every variant under `--below` bp folded into
+the reference. Indexed by gfa-to-tabix, the output is the coarse tier a graph
+track draws once zoomed out past the fine index, so a whole chromosome fits.
+[`gfa-to-tabix fold`](https://github.com/GMOD/gfa-to-tabix/blob/main/docs/subcommands.md#fold)
+documents the fold and the handover from the fine index.
+
+```console
+npx -p @jbrowse/bandage-core bandage-fold graph.rgfa.gz --below 10000 \
+  | gfa-to-tabix - -o graph.fold10000
+```
+
+- The input is a GFA or rGFA, plain or gzipped, or `-` for stdin. `-o out.gfa`
+  writes a file in place of stdout
+- `--reference PATH` names a plain GFA's backbone path. In an rGFA, the segments
+  tagged `SR:i:0` form the backbone
+- The fold keeps the backbone, every allele whose own length or the reference it
+  replaces reaches `--below`, and the shortest way from each one's ends back to
+  the backbone. It joins the reference between kept alleles into one segment
+- `bandage-fold` drops paths and walks from the output. It writes forward a
+  segment that a plain GFA's path reads reversed, and flips its links to match,
+  so the output re-reads as the graph that was folded
+- gfa-to-tabix's `--layout anchored|contig` should match the fine index's. An
+  anchored window inside a large bubble then returns the whole bubble in both
+  tiers, and a contig one only what links reach from it
+- The graph track folds each cut it draws at ten pixels (`FOLD_PX` in
+  jbrowse-plugin-graphgenomeviewer), and folding a fold again at a larger size
+  closely matches folding the original at that size. A tier folded at N and
+  handed over at N / 10 bp per pixel, such as
+  `coarse: { uri: "graph.fold10000", aboveBpPerPx: 1000 }`, therefore draws
+  nearly what the fine cut drew
+- Node caps a string at 512 MB, and `bandage-fold` reads the whole graph into
+  one, so it cannot fold a whole human pangenome. `gfa-to-tabix fold`, a port of
+  the same fold, writes the index in one pass:
+  `gfa-to-tabix fold graph.rgfa.gz --below 10000 -o graph.fold10000`
 
 ## Developing
 
@@ -64,21 +98,27 @@ pnpm test          # unit tests
 pnpm build         # dist/ with declarations
 ```
 
-The FMMM engine and its wasm build are in
-[graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout).
-
-CI also packs the core and runs the typecheck and tests of
-[BandageJS](https://github.com/cmdcolin/BandageJS) and
-[jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer)
-against it. For an API change, push the consumer's matching change to a
-`core-next` branch in that consumer's repo, which CI tests in place of `main`
-until the release.
-
-Release with `pnpm version patch`: it lints, tests, stamps `src/version.ts`,
-writes the changelog with git-cliff and pushes the `v*` tag. `publish.yml` then
-runs CI, consumers included, and publishes to npm with trusted publishing only
-if it passes. When a consumer fails, push its side to `core-next` and rerun the
-failed jobs.
+- The FMMM engine and its wasm build are in
+  [graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout)
+- CI also packs the core and runs the typecheck and tests of
+  [BandageJS](https://github.com/cmdcolin/BandageJS) and
+  [jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer)
+  against it. For an API change, push the consumer's matching change to a
+  `core-next` branch in that consumer's repo, which CI tests in place of `main`
+  until the release
+- `src/foldParity.test.ts` folds a few hundred random rGFA graphs with
+  `foldVariants` and with the gfa-to-tabix release that
+  `.github/actions/gfa-to-tabix` pins, and fails when they fold differently.
+  Locally the test runs the `gfa-to-tabix` on PATH or named by `GFA_TO_TABIX`,
+  and skips without one. In the other direction, gfa-to-tabix's
+  `scripts/parity-fold.sh` checks that `gfa-to-tabix fold` writes the same bytes
+  as `bandage-fold | gfa-to-tabix -`, and its CI tests the port against a pinned
+  bandage-core
+- Release with `pnpm version patch`: it lints, tests, stamps `src/version.ts`,
+  writes the changelog with git-cliff and pushes the `v*` tag. `publish.yml`
+  then runs CI, consumers included, and publishes to npm with trusted publishing
+  only if it passes. When a consumer fails, push its side to `core-next` and
+  rerun the failed jobs
 
 ## See also
 

package/dist/bubbles/bubbleHalos.js

@@ -1,17 +1,17 @@
 import {
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-BLDUBB7X.js";
-import "../chunks/chunk-AWJJSA7D.js";
+} from "../chunks/chunk-SZYFZNCO.js";
+import "../chunks/chunk-NWEVR2OQ.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-N73RA4DR.js";
+import "../chunks/chunk-AURNOR27.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-2VMKQKVO.js";
-import "../chunks/chunk-P276TWPM.js";
+import "../chunks/chunk-HNNP5QUN.js";
+import "../chunks/chunk-3GORESBG.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
-import "../chunks/chunk-VACK24HF.js";
+import "../chunks/chunk-JJV2GT2Z.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";

package/dist/bubbles/classifyBubble.js

@@ -3,16 +3,16 @@ import {
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "../chunks/chunk-AWJJSA7D.js";
+} from "../chunks/chunk-NWEVR2OQ.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-N73RA4DR.js";
+import "../chunks/chunk-AURNOR27.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-2VMKQKVO.js";
-import "../chunks/chunk-P276TWPM.js";
+import "../chunks/chunk-HNNP5QUN.js";
+import "../chunks/chunk-3GORESBG.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
-import "../chunks/chunk-VACK24HF.js";
+import "../chunks/chunk-JJV2GT2Z.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";

package/dist/bubbles/superbubbles.js

@@ -1,22 +1,22 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-KMLATBNT.js";
-import "../chunks/chunk-BLDUBB7X.js";
+} from "../chunks/chunk-J7RNXBXA.js";
+import "../chunks/chunk-SZYFZNCO.js";
 import "../chunks/chunk-RFG42VIO.js";
-import "../chunks/chunk-AWJJSA7D.js";
+import "../chunks/chunk-NWEVR2OQ.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-MHZTTLBU.js";
 import "../chunks/chunk-UAFATXYA.js";
 import "../chunks/chunk-VX656OAZ.js";
-import "../chunks/chunk-N73RA4DR.js";
+import "../chunks/chunk-AURNOR27.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-2VMKQKVO.js";
-import "../chunks/chunk-P276TWPM.js";
+import "../chunks/chunk-HNNP5QUN.js";
+import "../chunks/chunk-3GORESBG.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
-import "../chunks/chunk-VACK24HF.js";
+import "../chunks/chunk-JJV2GT2Z.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-K4KVAMEF.js → chunk-2A6Z2DHF.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-JVT3XTKN.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-4SN7R4UF.js → chunk-2MXFG3W7.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-JVT3XTKN.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {