@jbrowse/plugin-bed 2.17.0 → 3.0.0

package/esm/util.js

@@ -1,59 +1,58 @@
 import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMethylFeature';
-import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
 import { generateRepeatMaskerFeature, isRepeatMaskerDescriptionField, } from './generateRepeatMaskerFeature';
-function stringToStrand(f) {
-    if (f === '-1') {
-        return -1;
+import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
+function defaultParser(fields, splitLine) {
+    let hasBlockCount = false;
+    const r = [];
+    for (let i = 0; i < splitLine.length; i++) {
+        if (fields[i] === 'blockCount') {
+            hasBlockCount = true;
+        }
+        r.push([fields[i], splitLine[i]]);
     }
-    else if (f === '+') {
-        return 1;
+    const obj = Object.fromEntries(r);
+    if (hasBlockCount) {
+        const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
+        return {
+            ...rest,
+            blockStarts: arrayify(blockStarts),
+            chromStarts: arrayify(chromStarts),
+            blockSizes: arrayify(blockSizes),
+            thickStart: thickStart ? +thickStart : undefined,
+            thickEnd: thickEnd ? +thickEnd : undefined,
+            blockCount: blockCount ? +blockCount : undefined,
+        };
     }
     else {
-        return 0;
+        return obj;
     }
 }
-function defaultParser(fields, line) {
-    const obj = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
-    const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
-    return {
-        ...rest,
-        blockStarts: arrayify(blockStarts),
-        chromStarts: arrayify(chromStarts),
-        blockSizes: arrayify(blockSizes),
-        thickStart: thickStart ? +thickStart : undefined,
-        thickEnd: thickEnd ? +thickEnd : undefined,
-        blockCount: blockCount ? +blockCount : undefined,
-    };
-}
 export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
-    if (blockCount) {
-        const subfeatures = [];
-        const starts = chromStarts || blockStarts || [];
-        for (let b = 0; b < blockCount; b++) {
-            const bmin = (starts[b] || 0) + start;
-            const bsize = blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b];
-            if (bsize && bsize > 0) {
-                const bmax = bmin + bsize;
-                subfeatures.push({
-                    uniqueId: `${uniqueId}-${b}`,
-                    start: bmin,
-                    end: bmax,
-                    refName,
-                    type: 'block',
-                });
-            }
+    const subfeatures = [];
+    const starts = chromStarts || blockStarts || [];
+    for (let b = 0; b < blockCount; b++) {
+        const bmin = (starts[b] || 0) + start;
+        const bsize = blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b];
+        if (bsize && bsize > 0) {
+            const bmax = bmin + bsize;
+            subfeatures.push({
+                uniqueId: `${uniqueId}-${b}`,
+                start: bmin,
+                end: bmax,
+                refName,
+                type: 'block',
+            });
         }
-        return subfeatures;
     }
-    return [];
+    return subfeatures;
 }
 export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }) {
     const splitLine = line.split('\t');
     const refName = splitLine[colRef];
-    const start = +splitLine[colStart];
-    const end = +splitLine[colEnd] + (colStart === colEnd ? 1 : 0);
+    const start = Number.parseInt(splitLine[colStart], 10);
+    const end = Number.parseInt(splitLine[colEnd], 10) + (colStart === colEnd ? 1 : 0);
     return featureData2({
-        line,
+        splitLine,
         refName,
         start,
         end,
@@ -63,34 +62,35 @@ export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parse
         names,
     });
 }
-export function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
-    const splitLine = line.split('\t');
+export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
     const data = names
-        ? defaultParser(names, line)
-        : parser.parseLine(line, { uniqueId });
+        ? defaultParser(names, splitLine)
+        : parser.parseLine(splitLine, { uniqueId });
     const { strand: strand2, score: score2, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
-    const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
     const score = scoreColumn ? +data[scoreColumn] : score2 ? +score2 : undefined;
-    const strand = typeof strand2 === 'string' ? stringToStrand(strand2) : strand2;
-    const subfeatures = makeBlocks({
-        start,
-        uniqueId,
-        refName,
-        chromStarts,
-        blockCount,
-        blockSizes,
-        blockStarts,
-    });
+    const strand = typeof strand2 === 'string' ? (strand2 === '-' ? -1 : 1) : strand2;
+    const subfeatures = rest.blockCount
+        ? makeBlocks({
+            start,
+            uniqueId,
+            refName,
+            chromStarts: rest.chromStarts,
+            blockCount: rest.blockCount,
+            blockSizes: rest.blockSizes,
+            blockStarts: rest.blockStarts,
+        })
+        : undefined;
     if (isBedMethylFeature({ splitLine, start, end })) {
         return generateBedMethylFeature({
-            line,
+            splitLine,
             uniqueId,
             refName,
             start,
             end,
         });
     }
-    else if (isRepeatMaskerDescriptionField(description)) {
+    else if (isRepeatMaskerDescriptionField(rest.description)) {
+        const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
         return generateRepeatMaskerFeature({
             ...rest2,
             uniqueId,
@@ -104,7 +104,13 @@ export function featureData2({ line, refName, start, end, parser, uniqueId, scor
             subfeatures,
         });
     }
-    else if (isUcscTranscript({ strand, blockCount, thickStart })) {
+    else if (subfeatures &&
+        isUcscTranscript({
+            strand,
+            blockCount: rest.blockCount,
+            thickStart: rest.thickStart,
+        })) {
+        const { chromStarts, blockSizes, type, blockCount, thickStart, thickEnd, description, } = rest;
         return generateUcscTranscript({
             ...rest,
             description,
@@ -127,8 +133,6 @@ export function featureData2({ line, refName, start, end, parser, uniqueId, scor
         return {
             ...rest,
             uniqueId,
-            description,
-            type,
             score,
             start,
             end,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,10 +37,10 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^5.0.0",
+    "@gmod/bbi": "^6.0.0",
     "@gmod/bed": "^2.1.2",
-    "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/tabix": "^1.5.6"
+    "@gmod/bgzf-filehandle": "^2.0.1",
+    "@gmod/tabix": "^2.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }