Parsing a BAM file with javascript, yes we can. (Node.js and V8)
Node.js is an event-driven I/O server-side JavaScript environment based on V8, Google's open source JavaScript engine. In the current post I will describe how I've used Node/V8 to parse a BAM file. Here I've used node v0.5.5 and my code is hosted in a new git repository bionode.
Designing a C++ native extension for Node.js wrapping the bgzf format
BAM files are stored using the bgzf format. We must first create a C++ extension wrapping the methods related to bgzf. This process is nicely described in "Writing Node.js Native Extensions". Here, a BGZF* pointer is wrapped into a class BGZFSupport that extends v8::ObjectWrapp:class BGZFSupport: public ObjectWrap
{
private:
BGZF* file;
public:
(...)
int close()
{
int ret=0;
if(file!=NULL) ret=::bgzf_close(file);
file=NULL;
return ret;
}
~BGZFSupport()
{
if(file!=NULL) ::bgzf_close(file);
}
(...)
The javascript constructor for BGZFSupport opens the bgzfile and is implemented on the C++ side as: static Handle<Value> New(const Arguments& args)
{
HandleScope scope;
if (args.Length() < 2)
{
RETURN_THROW("Expected two parameters for bgfz");
}
if(!args[0]->IsString())
{
RETURN_THROW("1st argument is not a string");
}
if(!args[1]->IsString())
{
RETURN_THROW("2nd argument is not a string");
}
v8::String::Utf8Value filename(args[0]);
v8::String::Utf8Value mode(args[1]);
BGZF* file= ::bgzf_open(ToCString(filename),ToCString(mode));
if(file==NULL)
{
RETURN_THROW("Cannot open \"" << ToCString(filename) << "\"");
}
BGZFSupport* instance = new BGZFSupport(file);
instance->Wrap(args.This());
return args.This();
}
... and so on for the other functions...Implementing the javascript-based BAM-Reader
Next, we can embbed this BGZFSupport in a javascript file that will read a BAM file:var bgzf=require("bgzf");
and we create a javascript class/function BamReader that will open the file as bgzf and will read the BAM header:var bgzf=require("bgzf");
var Buffer = require('buffer').Buffer;
function BamReader(path)
{
this.fd= new bgzf.bgzf(path,"r");
var b=new Buffer(4);
var n = this.fd.read(b,0,4);
if(n!=4) throw new Error("Cannot read 4 bytes");
if(b[0]!=66) throw new Error("Error MAGIC[0]");
if(b[1]!=65) throw new Error("Error MAGIC[1] got"+b[1]);
if(b[2]!="M".charCodeAt(0)) throw new Error("Error MAGIC[2]");
if(b[3]!="\1".charCodeAt(0)) throw new Error("Error MAGIC[3]");
/* l_text */
n = this.fd.read(b,0,4);
if(n!=4) throw new Error("Cannot read 4 bytes");
var l_text=b.readInt32LE(0);
b=new Buffer(l_text);
n = this.fd.read(b,0,l_text);
if(n!=l_text) throw new Error("Cannot read "+l_text+" bytes (l_text)");
this.text=b.toString('utf-8', 0, l_text);
/* n_seq */
b=new Buffer(4);
n = this.fd.read(b,0,4);
if(n!=4) throw new Error("Cannot read 4 bytes");
var n_ref=b.readInt32LE(0);
this.references=[];
this.name2seq={};
for(var i=0;i< n_ref;++i)
{
var refseq={};
/* l_name */
b=new Buffer(4);
n = this.fd.read(b,0,4);
if(n!=4) throw new Error("Cannot read 4 bytes");
var l_name=b.readInt32LE(0);
/* name */
b=new Buffer(l_name);
n = this.fd.read(b,0,l_name);
if(n!=l_name) throw new Error("Cannot read "+l_name+" bytes (name)");
refseq.name=b.toString('utf-8', 0,l_name-1);//\0 terminated
/* l_ref */
b=new Buffer(4);
n = this.fd.read(b,0,4);
if(n!=4) throw new Error("Cannot read 4 bytes");
refseq.l_ref=b.readInt32LE(0);
this.references.push(refseq);
this.name2seq[refseq.name]=refseq;
}
//console.log(this.name2seq);
}
Another function next() reads the next alignment or returns null ( see the code ).Testing
$ export NODE_PATH=/path/to/bionode/build
the script reads a simple BAM file and prints the positions of the reads:
(...)
var r= new BamReader("/path/to/samtools-0.1.17/examples/toy.bam");
var align;
while((align=r.next())!=null)
{
console.log(
r.references[align.refID].name+"\t"+
align.read_name+"\t"+
align.pos
);
}
r.close();
Result
$ node bgzf.js ref r001 6 ref r002 8 ref r003 8 ref r004 15 ref r003 28 ref r001 36 ref2 x1 0 ref2 x2 1 ref2 x3 5 ref2 x4 9 ref2 x5 11 ref2 x6 13
Remaining questions:
At the moment, I don't know how to correctly package the C++ and javascript files for node.js, how to correctly include the files, how to group the different files under a common 'namespace', etc...That's It,
Pierre
