public static void Main(string[] args)
{
try {
PlatformManager.Services.MaxSequenceSize = int.MaxValue;
PlatformManager.Services.DefaultBufferSize = 4096;
PlatformManager.Services.Is64BitProcessType = true;
if (args.Length > 4) {
Console.WriteLine ("Too many arguments");
DisplayHelp ();
} else if (args.Length < 4) {
Console.WriteLine ("Not enough arguments");
DisplayHelp();
}else if (args [0] == "h" || args [0] == "help" || args [0] == "?" || args [0] == "-h") {
DisplayHelp ();
} else {
string subreads_name = args [0];
string ccs_name = args [1];
string ref_name = args [2];
string zmw = args[3];
// Validate files exist
for(int i = 0; i < 3; i++) {
var fname = args[i];
if (!File.Exists(fname)) {
Console.WriteLine ("Can't find file: " + fname);
return;
}
if (i < 2) {
//TODO: Add code to ensure BAM exists here
}
}
// Validate ZMW Number
int holeNumber;
bool converted = int.TryParse(zmw, out holeNumber);
if (!converted || holeNumber < 0) {
Console.WriteLine("Could not convert " + zmw +" into hole number >= 0");
}
Console.WriteLine("Loading Data ...");
// Get CCS Read
IntList zmws = new IntList();
zmws.Add(holeNumber);
//zmws.Add(133403);
DataSet dt = new DataSet(ccs_name);
var query = new ZmwQuery(zmws, dt);
var ccs = query.FirstOrDefault();
if (ccs == null) {
Console.WriteLine("Could not query hole number " + holeNumber + " from file " + ccs_name);
return;
}
var seq_str = ccs.Sequence();
var sequence = new Sequence(DnaAlphabet.Instance, seq_str);
sequence.ID = ccs.FullName();
//Clean up
query.Dispose(); query = null;
ccs.Dispose(); ccs = null;
dt.Dispose(); dt = null;
Console.WriteLine("Aligning Data ... ");
BWAPairwiseAligner bwa = new BWAPairwiseAligner(ref_name, false);
// Now get initial alignment and variants
BWAPairwiseAlignment aln = bwa.AlignRead(sequence) as BWAPairwiseAlignment;
if (aln == null) {
Console.WriteLine("Consensus read did not align");
return;
}
// Now get all the subreads
dt = new DataSet(subreads_name);
query = new ZmwQuery(zmws, dt);
// We must copy the data right away, or we wind up with a bunch of pointers that all hit the same thing
var subreads = query.Select(s => new Sequence(DnaAlphabet.Instance, s.Sequence()) {ID = s.FullName()}).ToList();
if (subreads.Count == 0 )
{
Console.WriteLine("Did not find any subreads from " + holeNumber + " in file " + subreads_name);
return;
}
subreads.ForEach( s => {
var split = s.ID.Split('/');
s.ID = String.Join("/", split.Skip(1)); });
zmws.Dispose(); zmws = null;
query.Dispose(); query = null;
// Now generate the dataset
var data = new CCSDataSet(sequence, subreads, aln);
Application.Init ();
MainWindow win = new MainWindow (data);
win.Show ();
Application.Run ();
}
}
catch(DllNotFoundException thrown) {
Console.WriteLine ("Error thrown when attempting to generate the CCS results.");
Console.WriteLine("A shared library was not found. To solve this, please add the folder" +
" with the downloaded files *.so and *.dylib " +
"to your environmental variables (LD_LIBRARY_PATH on Ubuntu, DYLD_LIBRARY_PATH on Mac OS X).");
Console.WriteLine ("Error: " + thrown.Message);
Console.WriteLine (thrown.StackTrace);
}
catch(Exception thrown) {
Console.WriteLine ("Error thrown when attempting to generate the CCS results");
Console.WriteLine ("Error: " + thrown.Message);
Console.WriteLine (thrown.StackTrace);
while (thrown.InnerException != null) {
Console.WriteLine ("Inner Exception: " + thrown.InnerException.Message);
thrown = thrown.InnerException;
}
}
}