Get started with pileup CDN

// Include the pileup library from the CDN
const Pileup = require('https://cdn.cdnhub.io/pileup/0.7.0/pileup.min.js');

// Read reference genome sequence
const reference = 'AGCTAGCTAGCTAGCTAGCT'; // Replace with your actual reference sequence

// Read BAM file and extract reads
const bamReader = new BAMReader('path/to/your/bamfile.bam');
const reads = [];

bamReader.on('read', (record) => {
  if (record.rname && record.seq) {
    reads.push({ name: record.rname, sequence: record.seq.toString() });
  }
});

bamReader.on('end', () => {
  // Perform pileup
  const pileupResult = Pileup.call(reference, reads);

  // Process pileup result
  const pileupColumns = pileupResult[0];
  const pileupRows = pileupResult[1];

  // Print pileup result for the first position as an example
  console.log('Position: 0');
  console.log('Reference:', reference[0]);
  console.log('Reads:');

  pileupColumns.forEach((column, i) => {
    console.log(`Read ${i + 1}:`, column.sequence[column.baseCall]);
  });

  pileupRows.forEach((row, i) => {
    console.log(`Read ${i + 1 + reads.length}:`, row.sequence);
  });
});