@jbrowse/img 4.2.0 → 4.3.0

package/README.md

@@ -99,11 +99,38 @@ jb2export --fasta data/volvox/volvox.fa \
   --loc ctgA:609..968
 ```
 
-You can see that instead of adding extra dash dash --flags, it is a colon based
-syntax that follows a track definition.
-
-The color and sort are specific to pileup, and height can apply to any track.
-More options may be described here soon
+Instead of extra `--flags`, track modifiers use a colon-based syntax that
+follows the track file argument. Full list of available modifiers:
+
+**All tracks**
+
+| Modifier     | Example      | Description                        |
+| ------------ | ------------ | ---------------------------------- |
+| `height:N`   | `height:400` | Track height in pixels             |
+| `force:true` | `force:true` | Render even if region is too large |
+
+**Alignment tracks (BAM/CRAM)**
+
+| Modifier                         | Example                                          | Description                                                                      |
+| -------------------------------- | ------------------------------------------------ | -------------------------------------------------------------------------------- |
+| `color:type` or `color:type:tag` | `color:strand`, `color:tag:XS`                   | Color scheme                                                                     |
+| `sort:type` or `sort:type:tag`   | `sort:strand`, `sort:tag:RG`                     | Sort reads                                                                       |
+| `featureHeight:preset\|N`        | `featureHeight:super-compact`, `featureHeight:4` | Per-read height. Presets: `normal` (7px), `compact` (2px), `super-compact` (1px) |
+| `noSpacing:true\|false`          | `noSpacing:true`                                 | Remove gap between reads                                                         |
+| `softClipping:true\|false`       | `softClipping:true`                              | Show soft-clipped bases                                                          |
+| `snpcov`                         | `snpcov`                                         | Render only the SNP/coverage subtrack                                            |
+
+**BigWig tracks**
+
+| Modifier                 | Example                | Description                                              |
+| ------------------------ | ---------------------- | -------------------------------------------------------- |
+| `autoscale:mode`         | `autoscale:localsd`    | Autoscale mode (`local`, `global`, `localsd`)            |
+| `minmax:min:max`         | `minmax:0:100`         | Manual score range                                       |
+| `scaletype:type`         | `scaletype:log`        | Scale type (`linear` or `log`)                           |
+| `fill:true\|false`       | `fill:false`           | Fill under curve                                         |
+| `crosshatch:true\|false` | `crosshatch:true`      | Draw crosshatches                                        |
+| `resolution:value`       | `resolution:superfine` | BigWig resolution (`fine`, `superfine`, or a multiplier) |
+| `color:colorname`        | `color:purple`         | Fill color                                               |
 
 ### Force render a large region
 

package/esm/renderRegion.js

@@ -303,6 +303,43 @@ function process(trackEntry, view, extra = c => c) {
                 display.setColor(type);
             }
         }
+        else if (opt.startsWith('featureHeight:')) {
+            const [, val] = opt.split(':');
+            if (val) {
+                const pileup = display.PileupDisplay ?? display;
+                if (val === 'normal') {
+                    pileup.setFeatureHeight(7);
+                    pileup.setNoSpacing(false);
+                }
+                else if (val === 'compact') {
+                    pileup.setFeatureHeight(2);
+                    pileup.setNoSpacing(true);
+                }
+                else if (val === 'super-compact') {
+                    pileup.setFeatureHeight(1);
+                    pileup.setNoSpacing(true);
+                }
+                else {
+                    const n = +val;
+                    if (isNaN(n)) {
+                        throw new Error(`Invalid featureHeight "${val}". Use normal, compact, super-compact, or a number.`);
+                    }
+                    pileup.setFeatureHeight(n);
+                }
+            }
+        }
+        else if (opt.startsWith('noSpacing:')) {
+            const [, val = 'true'] = opt.split(':');
+            const pileup = display.PileupDisplay ?? display;
+            pileup.setNoSpacing(booleanize(val));
+        }
+        else if (opt.startsWith('softClipping:')) {
+            const [, val = 'true'] = opt.split(':');
+            const pileup = display.PileupDisplay ?? display;
+            if (booleanize(val) !== pileup.showSoftClipping) {
+                pileup.toggleSoftClipping();
+            }
+        }
         else if (opt.startsWith('force:')) {
             const [, force] = opt.split(':');
             if (force) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "4.2.0",
+  "version": "4.3.0",
   "main": "esm/index.js",
   "types": "esm/index.d.ts",
   "repository": {
@@ -34,12 +34,12 @@
     "@types/yargs": "^17.0.35",
     "canvas": "^3.2.3",
     "jsdom": "29.0.2",
-    "react": "^19.2.5",
-    "react-dom": "^19.2.5",
+    "react": "^19.2.6",
+    "react-dom": "^19.2.6",
     "tmp": "^0.2.5",
     "yargs": "^18.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^4.2.0",
-    "@jbrowse/react-linear-genome-view2": "^4.2.0"
+    "@jbrowse/plugin-linear-genome-view": "^4.3.0",
+    "@jbrowse/react-linear-genome-view2": "^4.3.0"
   },
   "publishConfig": {
     "access": "public"