jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/util/clipboard.d.ts

@@ -0,0 +1,2 @@
+export declare function copyToClipboard(text: string, onSuccess?: () => void, onError?: (e: unknown) => void): Promise<void>;
+export declare function downloadAsFile(content: string, filename: string, onSuccess?: () => void, onError?: (e: unknown) => void): void;

package/dist/util/clipboard.js

@@ -0,0 +1,28 @@
+export async function copyToClipboard(text, onSuccess, onError) {
+    try {
+        await navigator.clipboard.writeText(text);
+        onSuccess?.();
+    }
+    catch (e) {
+        console.error(e);
+        onError?.(e);
+    }
+}
+export function downloadAsFile(content, filename, onSuccess, onError) {
+    try {
+        const url = URL.createObjectURL(new Blob([content], { type: 'text/plain' }));
+        const a = document.createElement('a');
+        a.href = url;
+        a.download = filename;
+        document.body.append(a);
+        a.click();
+        a.remove();
+        URL.revokeObjectURL(url);
+        onSuccess?.();
+    }
+    catch (e) {
+        console.error(e);
+        onError?.(e);
+    }
+}
+//# sourceMappingURL=clipboard.js.map

package/dist/util/clipboard.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"clipboard.js","sourceRoot":"","sources":["../../src/util/clipboard.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,IAAY,EACZ,SAAsB,EACtB,OAA8B;IAE9B,IAAI,CAAC;QACH,MAAM,SAAS,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QACzC,SAAS,EAAE,EAAE,CAAA;IACf,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,EAAE,CAAC,CAAC,CAAC,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,OAAe,EACf,QAAgB,EAChB,SAAsB,EACtB,OAA8B;IAE9B,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,GAAG,CAAC,eAAe,CAAC,IAAI,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QACrC,CAAC,CAAC,IAAI,GAAG,GAAG,CAAA;QACZ,CAAC,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACrB,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,KAAK,EAAE,CAAA;QACT,CAAC,CAAC,MAAM,EAAE,CAAA;QACV,GAAG,CAAC,eAAe,CAAC,GAAG,CAAC,CAAA;QACxB,SAAS,EAAE,EAAE,CAAA;IACf,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,EAAE,CAAC,CAAC,CAAC,CAAA;IACd,CAAC;AACH,CAAC"}

package/dist/util/fastaUtils.d.ts

@@ -6,11 +6,12 @@ import type { Feature, Region } from '@jbrowse/core/util';
  * @param selectedRegion - Optional region to extract
  * @returns FASTA formatted text
  */
-export declare function processFeaturesToFasta({ regions, showAllLetters, samples, features, }: {
+export declare function processFeaturesToFasta({ regions, showAllLetters, samples, features, includeInsertions, }: {
     regions: Region[];
     samples: Sample[];
     showAsUpperCase?: boolean;
     mismatchRendering?: boolean;
     showAllLetters?: boolean;
+    includeInsertions?: boolean;
     features: Map<string, Feature>;
 }): string[];

package/dist/util/fastaUtils.js

@@ -4,12 +4,15 @@
  * @param selectedRegion - Optional region to extract
  * @returns FASTA formatted text
  */
-export function processFeaturesToFasta({ regions, showAllLetters, samples, features, }) {
+export function processFeaturesToFasta({ regions, showAllLetters, samples, features, includeInsertions, }) {
     const region = regions[0];
     const sampleToRowMap = new Map(samples.map((s, i) => [s.id, i]));
     const rlen = region.end - region.start;
     // Use character arrays instead of strings for O(1) mutations
     const outputRowsArrays = samples.map(() => new Array(rlen).fill('-'));
+    // Track insertions at each position if includeInsertions is enabled
+    // Key is the reference position (0-based relative to region), value is array of insertions
+    const insertionsAtPosition = new Map();
     for (const feature of features.values()) {
         const leftCoord = feature.get('start');
         const vals = feature.get('alignments');
@@ -21,7 +24,7 @@ export function processFeaturesToFasta({ regions, showAllLetters, samples, featu
                 continue;
             }
             const rowArray = outputRowsArrays[row];
-            // Single-pass processing: handle gaps, matches, and mismatches together
+            // Single-pass processing: handle gaps, matches, mismatches, and collect insertions
             for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
                 if (seq[i] !== '-') {
                     const c = alignment[i];
@@ -48,6 +51,73 @@ export function processFeaturesToFasta({ regions, showAllLetters, samples, featu
                     }
                     o++;
                 }
+                else if (includeInsertions) {
+                    // This is an insertion (reference has gap)
+                    // Collect all consecutive insertion characters
+                    let insertionSequence = '';
+                    while (i < alignment.length && seq[i] === '-') {
+                        const c = alignment[i];
+                        insertionSequence += c !== '-' && c !== ' ' ? c : '-';
+                        i++;
+                    }
+                    i--; // Back up one since the outer loop will increment
+                    if (insertionSequence.length > 0) {
+                        // Position is relative to region start, insertions come after position o-1
+                        // (or before position 0 if o is 0)
+                        const insertPos = leftCoord + o - region.start;
+                        if (insertPos >= 0 && insertPos <= rlen) {
+                            const existing = insertionsAtPosition.get(insertPos) || [];
+                            existing.push({ sequence: insertionSequence, sampleIndex: row });
+                            insertionsAtPosition.set(insertPos, existing);
+                        }
+                    }
+                }
+            }
+        }
+    }
+    if (includeInsertions && insertionsAtPosition.size > 0) {
+        return expandWithInsertions(outputRowsArrays, insertionsAtPosition, samples.length);
+    }
+    // Convert character arrays back to strings
+    return outputRowsArrays.map(arr => arr.join(''));
+}
+/**
+ * Expand sequences to include insertions
+ * At each position with insertions, find the max insertion length,
+ * then expand all sequences by that amount
+ */
+function expandWithInsertions(outputRowsArrays, insertionsAtPosition, numSamples) {
+    // Sort insertion positions in descending order so we can insert from right to left
+    // without affecting earlier positions
+    const sortedPositions = [...insertionsAtPosition.keys()].sort((a, b) => b - a);
+    for (const pos of sortedPositions) {
+        const insertions = insertionsAtPosition.get(pos);
+        // Find max insertion length at this position
+        let maxLen = 0;
+        for (const ins of insertions) {
+            if (ins.sequence.length > maxLen) {
+                maxLen = ins.sequence.length;
+            }
+        }
+        // Create a map from sample index to insertion sequence
+        const sampleInsertions = new Map();
+        for (const ins of insertions) {
+            sampleInsertions.set(ins.sampleIndex, ins.sequence);
+        }
+        // Insert characters at this position for each sample
+        for (let sampleIdx = 0; sampleIdx < numSamples; sampleIdx++) {
+            const rowArray = outputRowsArrays[sampleIdx];
+            const insertionSeq = sampleInsertions.get(sampleIdx);
+            if (insertionSeq) {
+                // This sample has an insertion - add it, padded with gaps if needed
+                const paddedInsertion = insertionSeq.padEnd(maxLen, '-');
+                // Insert after position `pos`
+                rowArray.splice(pos, 0, ...paddedInsertion.split(''));
+            }
+            else {
+                // No insertion for this sample - fill with gaps
+                const gaps = new Array(maxLen).fill('-');
+                rowArray.splice(pos, 0, ...gaps);
             }
         }
     }

package/dist/util/fastaUtils.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fastaUtils.js","sourceRoot":"","sources":["../../src/util/fastaUtils.ts"],"names":[],"mappings":"AAUA;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CAAC,EACrC,OAAO,EACP,cAAc,EACd,OAAO,EACP,QAAQ,EACR,iBAAiB,GASlB;IACC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAChE,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAA;IAEtC,6DAA6D;IAC7D,MAAM,gBAAgB,GAAG,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;IAErE,oEAAoE;IACpE,2FAA2F;IAC3F,MAAM,oBAAoB,GAAG,IAAI,GAAG,EAA2B,CAAA;IAE/D,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAoC,CAAA;QACzE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAE9B,KAAK,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACjD,MAAM,SAAS,GAAG,GAAG,CAAC,GAAG,CAAA;YACzB,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACtC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YAED,MAAM,QAAQ,GAAG,gBAAgB,CAAC,GAAG,CAAE,CAAA;YAEvC,mFAAmF;YACnF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnB,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;oBACtB,MAAM,GAAG,GAAG,SAAS,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;oBAExC,IAAI,GAAG,IAAI,CAAC,IAAI,GAAG,GAAG,IAAI,EAAE,CAAC;wBAC3B,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BACd,MAAM;4BACN,QAAQ,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;wBACrB,CAAC;6BAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BACrB,IAAI,cAAc,EAAE,CAAC;gCACnB,kDAAkD;gCAClD,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;4BACnB,CAAC;iCAAM,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gCACxB,0BAA0B;gCAC1B,QAAQ,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;4BACrB,CAAC;iCAAM,CAAC;gCACN,4BAA4B;gCAC5B,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;4BACnB,CAAC;wBACH,CAAC;oBACH,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;qBAAM,IAAI,iBAAiB,EAAE,CAAC;oBAC7B,2CAA2C;oBAC3C,+CAA+C;oBAC/C,IAAI,iBAAiB,GAAG,EAAE,CAAA;oBAC1B,OAAO,CAAC,GAAG,SAAS,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBAC9C,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;wBACtB,iBAAiB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;wBACrD,CAAC,EAAE,CAAA;oBACL,CAAC;oBACD,CAAC,EAAE,CAAA,CAAC,kDAAkD;oBAEtD,IAAI,iBAAiB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;wBACjC,2EAA2E;wBAC3E,mCAAmC;wBACnC,MAAM,SAAS,GAAG,SAAS,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;wBAC9C,IAAI,SAAS,IAAI,CAAC,IAAI,SAAS,IAAI,IAAI,EAAE,CAAC;4BACxC,MAAM,QAAQ,GAAG,oBAAoB,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,EAAE,CAAA;4BAC1D,QAAQ,CAAC,IAAI,CAAC,EAAE,QAAQ,EAAE,iBAAiB,EAAE,WAAW,EAAE,GAAG,EAAE,CAAC,CAAA;4BAChE,oBAAoB,CAAC,GAAG,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;wBAC/C,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,iBAAiB,IAAI,oBAAoB,CAAC,IAAI,GAAG,CAAC,EAAE,CAAC;QACvD,OAAO,oBAAoB,CACzB,gBAAgB,EAChB,oBAAoB,EACpB,OAAO,CAAC,MAAM,CACf,CAAA;IACH,CAAC;IAED,2CAA2C;IAC3C,OAAO,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;AAClD,CAAC;AAED;;;;GAIG;AACH,SAAS,oBAAoB,CAC3B,gBAA4B,EAC5B,oBAAkD,EAClD,UAAkB;IAElB,mFAAmF;IACnF,sCAAsC;IACtC,MAAM,eAAe,GAAG,CAAC,GAAG,oBAAoB,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAE9E,KAAK,MAAM,GAAG,IAAI,eAAe,EAAE,CAAC;QAClC,MAAM,UAAU,GAAG,oBAAoB,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;QAEjD,6CAA6C;QAC7C,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,KAAK,MAAM,GAAG,IAAI,UAAU,EAAE,CAAC;YAC7B,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,GAAG,MAAM,EAAE,CAAC;gBACjC,MAAM,GAAG,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAA;YAC9B,CAAC;QACH,CAAC;QAED,uDAAuD;QACvD,MAAM,gBAAgB,GAAG,IAAI,GAAG,EAAkB,CAAA;QAClD,KAAK,MAAM,GAAG,IAAI,UAAU,EAAE,CAAC;YAC7B,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,WAAW,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAA;QACrD,CAAC;QAED,qDAAqD;QACrD,KAAK,IAAI,SAAS,GAAG,CAAC,EAAE,SAAS,GAAG,UAAU,EAAE,SAAS,EAAE,EAAE,CAAC;YAC5D,MAAM,QAAQ,GAAG,gBAAgB,CAAC,SAAS,CAAE,CAAA;YAC7C,MAAM,YAAY,GAAG,gBAAgB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YAEpD,IAAI,YAAY,EAAE,CAAC;gBACjB,oEAAoE;gBACpE,MAAM,eAAe,GAAG,YAAY,CAAC,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;gBACxD,8BAA8B;gBAC9B,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,EAAE,GAAG,eAAe,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;YACvD,CAAC;iBAAM,CAAC;gBACN,gDAAgD;gBAChD,MAAM,IAAI,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACxC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,EAAE,GAAG,IAAI,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;IAED,2CAA2C;IAC3C,OAAO,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;AAClD,CAAC"}

package/dist/util/fastaUtils.test.js

@@ -92,4 +92,194 @@ test('gap in assembly1', () => {
     });
     expect(result).toMatchSnapshot();
 });
+test('includeInsertions - single insertion in one sample', () => {
+    // Reference seq has a gap (insertion in assembly2)
+    // seq:       AC--GTAC (reference with gap = insertion in aligned seq)
+    // assembly1: AC--GTAC (no insertion, matches reference gap)
+    // assembly2: ACTTGTAC (has TT insertion)
+    const mockFeature = new SimpleFeature({
+        uniqueId: '123',
+        refName: 'abc',
+        start: 100,
+        end: 106, // 6 bp reference (AC GTAC without the gap)
+        seq: 'AC--GTAC',
+        alignments: {
+            assembly1: {
+                chr: 'chr1',
+                start: 100,
+                seq: 'AC--GTAC',
+                strand: 1,
+            },
+            assembly2: {
+                chr: 'chr2',
+                start: 200,
+                seq: 'ACTTGTAC',
+                strand: 1,
+            },
+        },
+    });
+    const result = processFeaturesToFasta({
+        features: makeMap([mockFeature]),
+        samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+        includeInsertions: true,
+        showAllLetters: true,
+        regions: [
+            {
+                refName: 'chr1',
+                start: 100,
+                end: 106,
+                assemblyName: 'assembly1',
+            },
+        ],
+    });
+    // assembly1 should have gaps where the insertion is
+    // assembly2 should have the TT insertion
+    expect(result).toMatchSnapshot();
+});
+test('includeInsertions - insertions in multiple samples with different lengths', () => {
+    // Reference has gap, different samples have different insertion lengths
+    // seq:       AC---GTAC (reference with 3-bp gap)
+    // assembly1: AC-T-GTAC (has T insertion, 1 bp)
+    // assembly2: ACTTTGTAC (has TTT insertion, 3 bp)
+    const mockFeature = new SimpleFeature({
+        uniqueId: '123',
+        refName: 'abc',
+        start: 100,
+        end: 106,
+        seq: 'AC---GTAC',
+        alignments: {
+            assembly1: {
+                chr: 'chr1',
+                start: 100,
+                seq: 'AC-T-GTAC',
+                strand: 1,
+            },
+            assembly2: {
+                chr: 'chr2',
+                start: 200,
+                seq: 'ACTTTGTAC',
+                strand: 1,
+            },
+        },
+    });
+    const result = processFeaturesToFasta({
+        features: makeMap([mockFeature]),
+        samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+        includeInsertions: true,
+        showAllLetters: true,
+        regions: [
+            {
+                refName: 'chr1',
+                start: 100,
+                end: 106,
+                assemblyName: 'assembly1',
+            },
+        ],
+    });
+    // assembly1 should have T-- (padded to max insertion length 3)
+    // assembly2 should have TTT
+    expect(result).toMatchSnapshot();
+});
+test('includeInsertions - insertions at multiple positions', () => {
+    // Reference has gaps at two positions
+    // seq:       A-CG-TAC
+    // assembly1: ATCGGTAC (T insertion at pos 1, G insertion at pos 4)
+    // assembly2: A-CG-TAC (no insertions)
+    const mockFeature = new SimpleFeature({
+        uniqueId: '123',
+        refName: 'abc',
+        start: 100,
+        end: 106,
+        seq: 'A-CG-TAC',
+        alignments: {
+            assembly1: {
+                chr: 'chr1',
+                start: 100,
+                seq: 'ATCGGTAC',
+                strand: 1,
+            },
+            assembly2: {
+                chr: 'chr2',
+                start: 200,
+                seq: 'A-CG-TAC',
+                strand: 1,
+            },
+        },
+    });
+    const result = processFeaturesToFasta({
+        features: makeMap([mockFeature]),
+        samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+        includeInsertions: true,
+        showAllLetters: true,
+        regions: [
+            {
+                refName: 'chr1',
+                start: 100,
+                end: 106,
+                assemblyName: 'assembly1',
+            },
+        ],
+    });
+    expect(result).toMatchSnapshot();
+});
+test('includeInsertions=false ignores insertions', () => {
+    const mockFeature = new SimpleFeature({
+        uniqueId: '123',
+        refName: 'abc',
+        start: 100,
+        end: 106,
+        seq: 'AC--GTAC',
+        alignments: {
+            assembly1: {
+                chr: 'chr1',
+                start: 100,
+                seq: 'AC--GTAC',
+                strand: 1,
+            },
+            assembly2: {
+                chr: 'chr2',
+                start: 200,
+                seq: 'ACTTGTAC',
+                strand: 1,
+            },
+        },
+    });
+    const result = processFeaturesToFasta({
+        features: makeMap([mockFeature]),
+        samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+        includeInsertions: false,
+        showAllLetters: true,
+        regions: [
+            {
+                refName: 'chr1',
+                start: 100,
+                end: 106,
+                assemblyName: 'assembly1',
+            },
+        ],
+    });
+    // Without insertions, both should be 6 characters (no expansion)
+    expect(result[0]).toHaveLength(6);
+    expect(result[1]).toHaveLength(6);
+    expect(result).toMatchSnapshot();
+});
+test('includeInsertions with no insertions present', () => {
+    // No gaps in reference = no insertions
+    const result = processFeaturesToFasta({
+        features: makeMap([mockFeature]),
+        samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+        includeInsertions: true,
+        showAllLetters: true,
+        regions: [
+            {
+                refName: 'chr1',
+                start: 100,
+                end: 105,
+                assemblyName: 'assembly1',
+            },
+        ],
+    });
+    // Should behave same as without includeInsertions since there are none
+    expect(result).toMatchSnapshot();
+});
 //# sourceMappingURL=fastaUtils.test.js.map

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package/dist/util/parseAssemblyName.d.ts

@@ -0,0 +1,32 @@
+export interface ParsedAssemblyName {
+    assemblyName: string;
+    chr: string;
+}
+/**
+ * Parses assembly name and chromosome from a combined string in MAF tabix format.
+ *
+ * Handles multiple formats:
+ * - Single string with no dots: assemblyName is the entire string, chr is empty
+ * - `assembly.chr`: Single dot separates assembly name from chromosome
+ * - `assembly.version.chr`: Two dots where middle part is numeric (version number)
+ *   - assemblyName includes the version (e.g., "hg38.1" from "hg38.1.chr1")
+ * - `assembly.chr.more`: Two dots where middle part is non-numeric
+ *   - assemblyName is first part, chr includes rest (e.g., "mm10" and "chr1.random")
+ */
+export declare function parseAssemblyAndChr(assemblyAndChr: string): ParsedAssemblyName;
+/**
+ * Parses assembly name and chromosome from a combined string in BigMaf format.
+ *
+ * Uses simple dot splitting: org.chr where org is before the first dot,
+ * chr is everything after the first dot.
+ */
+export declare function parseAssemblyAndChrSimple(organismChr: string): ParsedAssemblyName;
+/**
+ * Selects the appropriate sequence from alignments based on the lookup order:
+ * 1. refAssemblyName config value (if provided)
+ * 2. query.assemblyName (from the region being queried)
+ * 3. firstAssemblyNameFound (fallback to first assembly in data)
+ */
+export declare function selectReferenceSequence(alignments: Record<string, {
+    seq: string;
+}>, refAssemblyName: string | undefined, queryAssemblyName: string | undefined, firstAssemblyNameFound: string | undefined): string | undefined;

package/dist/util/parseAssemblyName.js

@@ -0,0 +1,87 @@
+/**
+ * Parses assembly name and chromosome from a combined string in MAF tabix format.
+ *
+ * Handles multiple formats:
+ * - Single string with no dots: assemblyName is the entire string, chr is empty
+ * - `assembly.chr`: Single dot separates assembly name from chromosome
+ * - `assembly.version.chr`: Two dots where middle part is numeric (version number)
+ *   - assemblyName includes the version (e.g., "hg38.1" from "hg38.1.chr1")
+ * - `assembly.chr.more`: Two dots where middle part is non-numeric
+ *   - assemblyName is first part, chr includes rest (e.g., "mm10" and "chr1.random")
+ */
+export function parseAssemblyAndChr(assemblyAndChr) {
+    const firstDotIndex = assemblyAndChr.indexOf('.');
+    if (firstDotIndex === -1) {
+        return {
+            assemblyName: assemblyAndChr,
+            chr: '',
+        };
+    }
+    const secondDotIndex = assemblyAndChr.indexOf('.', firstDotIndex + 1);
+    if (secondDotIndex === -1) {
+        return {
+            assemblyName: assemblyAndChr.slice(0, firstDotIndex),
+            chr: assemblyAndChr.slice(firstDotIndex + 1),
+        };
+    }
+    const secondPart = assemblyAndChr.slice(firstDotIndex + 1, secondDotIndex);
+    const isNumeric = secondPart.length > 0 && !Number.isNaN(+secondPart);
+    if (isNumeric) {
+        return {
+            assemblyName: assemblyAndChr.slice(0, secondDotIndex),
+            chr: assemblyAndChr.slice(secondDotIndex + 1),
+        };
+    }
+    return {
+        assemblyName: assemblyAndChr.slice(0, firstDotIndex),
+        chr: assemblyAndChr.slice(firstDotIndex + 1),
+    };
+}
+/**
+ * Parses assembly name and chromosome from a combined string in BigMaf format.
+ *
+ * Uses simple dot splitting: org.chr where org is before the first dot,
+ * chr is everything after the first dot.
+ */
+export function parseAssemblyAndChrSimple(organismChr) {
+    const dotIndex = organismChr.indexOf('.');
+    if (dotIndex === -1) {
+        return {
+            assemblyName: organismChr,
+            chr: '',
+        };
+    }
+    return {
+        assemblyName: organismChr.slice(0, dotIndex),
+        chr: organismChr.slice(dotIndex + 1),
+    };
+}
+/**
+ * Selects the appropriate sequence from alignments based on the lookup order:
+ * 1. refAssemblyName config value (if provided)
+ * 2. query.assemblyName (from the region being queried)
+ * 3. firstAssemblyNameFound (fallback to first assembly in data)
+ */
+export function selectReferenceSequence(alignments, refAssemblyName, queryAssemblyName, firstAssemblyNameFound) {
+    let entry;
+    if (refAssemblyName) {
+        entry = alignments[refAssemblyName];
+        if (entry) {
+            return entry.seq;
+        }
+    }
+    if (queryAssemblyName) {
+        entry = alignments[queryAssemblyName];
+        if (entry) {
+            return entry.seq;
+        }
+    }
+    if (firstAssemblyNameFound) {
+        entry = alignments[firstAssemblyNameFound];
+        if (entry) {
+            return entry.seq;
+        }
+    }
+    return undefined;
+}
+//# sourceMappingURL=parseAssemblyName.js.map

package/dist/util/parseAssemblyName.js.map

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package/dist/util/parseAssemblyName.test.d.ts

@@ -0,0 +1 @@
+export {};