@jbrowse/plugin-bed 2.16.0 → 2.17.0

package/esm/util.js

@@ -1,173 +1,147 @@
-import { SimpleFeature } from '@jbrowse/core/util';
-export function ucscProcessedTranscript(feature) {
-    const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
-    if (!thickStart || !thickEnd || !strand) {
-        return feature;
+import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMethylFeature';
+import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
+import { generateRepeatMaskerFeature, isRepeatMaskerDescriptionField, } from './generateRepeatMaskerFeature';
+function stringToStrand(f) {
+    if (f === '-1') {
+        return -1;
+    }
+    else if (f === '+') {
+        return 1;
+    }
+    else {
+        return 0;
     }
-    const subfeatures = [];
-    oldSubfeatures
-        .filter(child => child.type === 'block')
-        .sort((a, b) => a.start - b.start)
-        .forEach(block => {
-        const start = block.start;
-        const end = block.end;
-        if (thickStart >= end) {
-            // left-side UTR
-            const prime = strand > 0 ? 'five' : 'three';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            // UTR | CDS
-            const prime = strand > 0 ? 'five' : 'three';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                start: thickStart,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd >= end) {
-            // CDS
-            subfeatures.push({
-                type: 'CDS',
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd < end) {
-            // UTR | CDS | UTR
-            const leftPrime = strand > 0 ? 'five' : 'three';
-            const rightPrime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: `${leftPrime}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                start: thickStart,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${rightPrime}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            // CDS | UTR
-            const prime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: 'CDS',
-                start,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${prime}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickEnd <= start) {
-            // right-side UTR
-            const prime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-    });
-    return { ...rest, strand, type: 'mRNA', refName, subfeatures };
 }
 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: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
-        chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
-        blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
+        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, }) {
-    const subfeatures = [];
-    const starts = chromStarts || blockStarts || [];
-    for (let b = 0; b < blockCount; b++) {
-        const bmin = (starts[b] || 0) + start;
-        const bmax = bmin + (blockSizes[b] || 0);
-        subfeatures.push({
-            uniqueId: `${uniqueId}-${b}`,
-            start: bmin,
-            end: bmax,
-            refName,
-            type: 'block',
-        });
+    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',
+                });
+            }
+        }
+        return subfeatures;
     }
-    return subfeatures;
+    return [];
 }
-export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
-    const l = line.split('\t');
-    const refName = l[colRef];
-    const start = +l[colStart];
-    const colSame = colStart === colEnd ? 1 : 0;
-    const end = +l[colEnd] + colSame;
+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);
+    return featureData2({
+        line,
+        refName,
+        start,
+        end,
+        parser,
+        uniqueId,
+        scoreColumn,
+        names,
+    });
+}
+export function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
+    const splitLine = line.split('\t');
     const data = names
         ? defaultParser(names, line)
         : parser.parseLine(line, { uniqueId });
-    const { blockCount, blockSizes, blockStarts, chromStarts, thickStart, thickEnd, type, score, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
-    const subfeatures = blockCount
-        ? makeBlocks({
+    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,
+    });
+    if (isBedMethylFeature({ splitLine, start, end })) {
+        return generateBedMethylFeature({
+            line,
+            uniqueId,
+            refName,
             start,
+            end,
+        });
+    }
+    else if (isRepeatMaskerDescriptionField(description)) {
+        return generateRepeatMaskerFeature({
+            ...rest2,
             uniqueId,
+            description,
+            type,
+            score,
+            start,
+            end,
+            strand,
             refName,
+            subfeatures,
+        });
+    }
+    else if (isUcscTranscript({ strand, blockCount, thickStart })) {
+        return generateUcscTranscript({
+            ...rest,
+            description,
             chromStarts,
-            blockCount,
+            thickStart,
+            thickEnd,
             blockSizes,
-            blockStarts,
-        })
-        : [];
-    const f = {
-        ...rest,
-        type,
-        score: scoreColumn ? +data[scoreColumn] : score,
-        start,
-        end,
-        refName,
-        uniqueId,
-        subfeatures,
-    };
-    return new SimpleFeature({
-        id: uniqueId,
-        data: isUcscProcessedTranscript(data)
-            ? ucscProcessedTranscript({
-                thickStart: thickStart,
-                thickEnd: thickEnd,
-                blockCount: blockCount,
-                blockSizes: blockSizes,
-                chromStarts: chromStarts,
-                ...f,
-            })
-            : f,
-    });
+            blockCount,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            uniqueId,
+            subfeatures,
+        });
+    }
+    else {
+        return {
+            ...rest,
+            uniqueId,
+            description,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            subfeatures,
+        };
+    }
 }
-export function isUcscProcessedTranscript(f) {
-    return f.thickStart && f.blockCount && f.strand !== 0;
+export function arrayify(f) {
+    return f !== undefined
+        ? typeof f === 'string'
+            ? f.split(',').map(f => +f)
+            : f
+        : undefined;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }