bedjs/lib/collapse.js

Manage BED (Browser Extensible Data) files with Node.JS (Bioinformatics)

//Collapse a bed object by region
module.exports.ByRegion = function(bed)
{
  //Collapsed array
  var out = [];

  //Read all the bed objects
  for(var i = 0; i < bed.length; i++)
  {
    //Get the bed object
    var obj = bed[i];

    //Check for inserted
    var inserted = false;

    //Read all the collapsed regions
    for(var j = 0; j < out.length; j++)
    {
      //Check the chromosome
      if(obj.chromosome !== out[j].chromosome){ continue; }

      //Check the start position
      if(obj.start > out[j].end){ continue; }

      //Check the end position
      if(obj.end < out[j].start){ continue; }

      //Check the strand
      if(typeof obj.strand !== 'undefined' && typeof out[j].strand !== 'undefined')
      {
        //Check the strands
        if(obj.strand !== out[j].strand){ continue; }
      }

      //Update the start position
      out[j].start = Math.min(out[j].start, obj.start);

      //Update the end position
      out[j].end = Math.max(out[j].end, obj.end);

      //Update the names
      if(typeof obj.name !== 'undefined')
      {
        //Check the out name
        if(typeof out[j].name === 'undefined'){ out[j].name = []; }

        //Check the index
        if(out[j].name.indexOf(obj.name) === -1){ out[j].name.push(obj.name); };
      }

      //Set inserted as true
      inserted = true;

      //Exit loop
      break;
    }

    //Check inserted
    if(inserted === true){ continue; }

    //Else, insert the region
    out.push(obj);

    //Get the last index
    var last = out.length - 1;

    //Update the name
    if(out[last].name !== 'undefined'){ out[last].name = out[last].name.split(','); }
  }

  //Join all the regions names
  for(var i = 0; i < out.length; i++)
  {
    //Check the name
    if(typeof out[i].name === 'undefined'){ continue; }

    //Update the names
    out[i].name = out[i].name.join(',');
  }

  //Return the collapsed array
  return out;
};

//Collapse a bed object by name
module.exports.ByName = function(bed)
{
  //Collapsed object
  var collapsed = { list: [], names: {} };

  //Read all the bed objects
  for(var i = 0; i < bed.length; i++)
  {
    //Get the bed object
    var obj = bed[i];

    //Check the name
    if(typeof obj.name === 'undefined')
    {
      //Show error
      console.log('ERROR: all bed objects must have a name if you want to collapse them by name...');

      //Exit
      return [];
    }

    //Find the name
    if(typeof collapsed.names[obj.name] === 'undefined')
    {
      //Save the region
      collapsed.list.push(obj);

      //Save the name and the index
      collapsed.names[obj.name] = collapsed.list.length - 1;

      //Next bed object
      continue;
    }

    //Get the output index
    var index = collapsed.names[obj.name];

    //Update the start position
    collapsed.list[index].start = Math.min(collapsed.list[index].start, obj.start);

    //Update the end position
    collapsed.list[index].end = Math.max(collapsed.list[index].end, obj.end);
  }

  //Return the new list
  return collapsed.list;
};