<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
<script type="module">
// Initialize Aioli with samtools v1.10
const CLI = await new Aioli("samtools/1.10");

// Show reads from toy.sam with flag "16". Try replacing "-f 16" with "-f 0".
const output = await CLI.exec("samtools view -f 16 /samtools/examples/toy.sam");
console.log(output);
</script>

<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
<script type="module">
// Note: `script type="module"` lets us use top-level await statements
const CLI = await new Aioli(["samtools/1.10", "seqtk/1.2"]);

// Here we write to a file with one tool, and use it as input for another tool!
// Convert a ".sam" file to a ".fastq", and save the result to "./toy.fastq"
let output = await CLI.exec("samtools fastq -o toy.fastq /samtools/examples/toy.sam");

// Run the tool "seqtk" on "toy.fastq" to generate QC metrics
output = await CLI.exec("seqtk fqchk toy.fastq");
console.log(output);
</script>

<input id="myfile" type="file" multiple>

<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
<script type="module">
const CLI = await new Aioli("samtools/1.10");
const output = await CLI.exec("samtools --version-only");
console.log(`Loaded ${output}`);

// Get the SAM file header when user selects a file from their computer
async function runSamtools(event) {
    // First, mount the file(s) to a virtual file system
    const files = event.target.files;
    // The function `.mount()` returns the absolute paths of each file mounted
    const paths = await CLI.mount(files);

    // List files in the current folder
    console.log("ls:", await CLI.ls("."));
    // Get info about the file we mounted (e.g. size, timestamp)
    console.log(`ls ${files[0].name}:`, await CLI.ls(paths[0]));

    // Retrieve SAM header on the first file the user selected
    const output = await CLI.exec(`samtools view -H ${files[0].name}`);
    console.log(output);
}

document.getElementById("myfile").addEventListener("change", runSamtools, false);
</script>

<script src="https://cdn.biowasm.com/v2/aioli/latest/aioli.js"></script>
<script type="module">
const CLI = await new Aioli("samtools/1.10");

// Mount a .bam and .bai from the 1000 Genomes Project. This lazy-mounts the URLs
// on the virtual file system, i.e. no data is downloaded yet.
const paths = await CLI.mount([
    "https://1000genomes.s3.amazonaws.com/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam",
    "https://1000genomes.s3.amazonaws.com/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam.bai"
]);

// Since the .bai index file is present, samtools only downloads a subset of the .bam!
// Check the "Network" tab in the developer console to confirm that.
const output = await CLI.exec(`samtools view ${paths[0]} 20:39,352,829-39,352,842`);
console.log(output);
</script>