testBAM.js

import BamReader from "../js/bam/bamReader.js";

function runBAMTests() {

    QUnit.test("BAM alignments", function (assert) {

        var done = assert.async();

        const chr = 'chr1';
        const bpStart = 155140000;
        const bpEnd = 155160000;

        const bamReader = new BamReader({
            type: 'bam',
            url: 'data/bam/na12889.bam',
            indexURL: 'data/bam/na12889.bam.bai'
        });

        let bamAlignments;

        bamReader.readAlignments(chr, bpStart, bpEnd)

            .then(function (alignmentContainer) {

                assert.ok(alignmentContainer);

                // 2 alignments, 1 paired and 1 single
                assert.equal(alignmentContainer.alignments.length, 2);

                const firstAlignment = alignmentContainer.alignments[0].firstAlignment;

                assert.equal(firstAlignment.seq, 'TTCATCTAAAAATCACATTGCAAATTATTCAATATATTTGGGCCTCCATCTCGTTTACATCAATATGTGTTTGTTGAAGTATCTGCCCTGCAATGTCCATA');

                assert.deepEqual(firstAlignment.qual, [34, 9, 12, 10, 24, 17, 10, 5, 19, 7, 28, 17, 23, 29, 10,
                    26, 10, 8, 14, 7, 15, 17, 32, 33, 31, 23, 34, 16, 33, 28, 34, 27, 10, 29, 10, 17, 11, 26,
                    8, 27, 4, 4, 35, 32, 12, 32, 40, 39, 38, 41, 40, 36, 3, 34, 17, 30, 37, 10, 29, 36, 41,
                    35, 24, 34, 11, 19, 11, 16, 24, 16, 26, 10, 11, 19, 13, 18, 11, 28, 30, 37, 30, 38, 43,
                    43, 40, 43, 43, 41, 32, 34, 39, 41, 31, 37, 36, 36, 36, 33, 37, 34, 30]);

                assert.equal(firstAlignment.start, 155148856);
                assert.equal(firstAlignment.scStart, 155148856 - 20);
                assert.equal(firstAlignment.lengthOnRef, 81);
                assert.equal(firstAlignment.scLengthOnRef, 101);
                assert.equal(firstAlignment.pairOrientation, 'F2R1');
                assert.equal(firstAlignment.fragmentLength, 307);
                assert.equal(firstAlignment.mq, 29);

                const blocks = firstAlignment.blocks;
                assert.equal(blocks.length, 4);
                const expectedLength = [20, 46, 8, 24];
                const expectedOffset = [0, 20, 66, 77];
                const expectedTypes = ['S', 'M', 'M', 'M'];
                for (let i = 0; i < 4; i++) {
                    const b = blocks[i];
                    assert.equal(b.len, expectedLength[i]);
                    assert.equal(b.type, expectedTypes[i]);
                    assert.equal(b.seqOffset, expectedOffset[i]);
                }

                const insertions = firstAlignment.insertions;
                assert.equal(insertions.length, 1);
                assert.equal(insertions[0].len, 3);
                assert.equal(insertions[0].type, 'I');

                const tags = firstAlignment.tags();
                assert.equal(tags["BQ"], "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@TPEO@@KPXPZJKS@@@@@@@@@@@@@@@@@@@@@@@@@@@");
                assert.equal(tags["AM"], 29);
                assert.equal(tags["MQ"], 29);
                assert.equal(tags["AM"], 29);
                assert.equal(tags["XT"], "M");

                done();
            })


            .catch(function (error) {
                console.error(error);
                assert.ok(false, error);  // failed

            });

    });


}

export default runBAMTests;