Merge pull request #20459 from jmchilton/auto_pairing_fix

- doc: Simple _R1 _R2 fastqs split.

  inputs:

  - input_R1.fastq

  - input_R2.fastq

  paired:

    input:

      forward: input_R1.fastq

      reverse: input_R2.fastq

- doc: Compressed _R1 _R2 fastqs split.

  inputs:

  - input_R1.fastq.gz

  - input_R2.fastq.gz

  paired:

    input:

      forward: input_R1.fastq.gz

      reverse: input_R2.fastq.gz

- doc: Joining common prefixes on _R1 _R2.

  inputs:

  - input541_R1.fastq

  - input541_R2.fastq

  - input521_R1.fastq

  - input521_R2.fastq

  paired:

    input541:

      forward: input541_R1.fastq

      reverse: input541_R2.fastq

    input521:

      forward: input521_R1.fastq

      reverse: input521_R2.fastq

- doc: Simple .1.fastq/.2.fastq split.

  inputs:

  - input.1.fastq

  - input.2.fastq

  paired:

    input:

      forward: input.1.fastq

      reverse: input.2.fastq

- doc: Simple .1.fastq.gz/.2.fastq.gz split.

  inputs:

  - input.1.fastq.gz

  - input.2.fastq.gz

  paired:

    input:

      forward: input.1.fastq.gz

      reverse: input.2.fastq.gz

- doc: Simple _1/_2 split.

  inputs:

  - input_1.fastq

  - input_2.fastq

  paired:

    input:

      forward: input_1.fastq

      reverse: input_2.fastq

- doc: Simple _1/_2 split on compressed files (.gz)

  inputs:

  - input_1.fastq.gz

  - input_2.fastq.gz

  paired:

    input:

      forward: input_1.fastq.gz

      reverse: input_2.fastq.gz

- doc: Simple _1/_2 split on compressed files (.bz2)

  inputs:

  - input_1.fastq.bz2

  - input_2.fastq.bz2

  paired:

    input:

      forward: input_1.fastq.bz2

      reverse: input_2.fastq.bz2

import AUTO_PAIRING_SPECIFICATION from "./auto_pairing_spec.yml";

import {

    autoDetectPairs,

    autoPairWithCommonFilters,

        expect(summary.pairs).toHaveLength(0);

    });

});

interface ExpectedPair {

    name: string;

    forward: string;

    reverse: string;

}

interface AutoPairingTest {

    doc?: string;

    inputs: string[];

    paired: Record<string, ExpectedPair>;

}

describe("fulfills auto pairing specification ", () => {

    test("the specification", () => {

        const tests = AUTO_PAIRING_SPECIFICATION;

        tests.forEach((test: AutoPairingTest) => {

            const inputs = test.inputs.map((name) => mockDataset(name));

            const summary = autoPairWithCommonFilters(inputs, true);

            for (const name in test.paired) {

                const expectedPair = test.paired[name] as ExpectedPair;

                const pair = summary.pairs?.find((p) => p.name === name);

                expect(pair).toBeDefined();

                expect(pair?.forward.name).toEqual(expectedPair.forward);

                expect(pair?.reverse.name).toEqual(expectedPair.reverse);

            }

        });

    });

});

    if (willRemoveExtensions) {

        const lastDotIndex = lcs.lastIndexOf(".");

        if (lastDotIndex > 0) {

            const extension = lcs.slice(lastDotIndex, lcs.length);

            let extension = lcs.slice(lastDotIndex, lcs.length);

            if ([".gz", ".bz", ".bzip", ".bz2"].indexOf(extension) !== -1) {

                const secondLastDotIndex = lcs.lastIndexOf(".", lastDotIndex - 1);

                if (secondLastDotIndex > 0) {

                    extension = lcs.slice(secondLastDotIndex, lcs.length);

                }

            }

            lcs = lcs.replace(extension, "");

            fwdName = fwdName.replace(extension, "");

            revName = revName.replace(extension, "");