public static void Main(string[] args)
{
try {
PlatformManager.Services.MaxSequenceSize = int.MaxValue;
PlatformManager.Services.DefaultBufferSize = 4096;
PlatformManager.Services.Is64BitProcessType = true;
if (args.Length > 3) {
Console.WriteLine ("Too many arguments");
DisplayHelp ();
} else if (args.Length < 2) {
Console.WriteLine("Not enough arguments");
DisplayHelp();
}else if (args [0] == "h" || args [0] == "help" || args [0] == "?" || args [0] == "-h") {
DisplayHelp ();
} else {
string bam_name = args [0];
string out_dir = args [1];
string ref_name = args.Length > 2 ? args [2] : null;
if (!File.Exists(bam_name)) {
Console.WriteLine ("Can't find file: " + bam_name);
return;
}
if (ref_name != null && !File.Exists (ref_name)) {
Console.WriteLine ("Can't find file: " + ref_name);
return;
}
if (Directory.Exists (out_dir)) {
Console.WriteLine ("The output directory already exists, please specify a new directory or delete the old one.");
return;
}
Directory.CreateDirectory (out_dir);
List<CCSReadMetricsOutputter> outputters = new List<CCSReadMetricsOutputter> () {
new ZmwOutputFile(out_dir),
new ZScoreOutputter(out_dir),
new VariantOutputter(out_dir),
new SNROutputFile(out_dir),
new QVCalibration(out_dir)};
PacBioCCSBamReader bamreader = new PacBioCCSBamReader ();
BWAPairwiseAligner bwa = null;
bool callVariants = ref_name != null;
if(callVariants) {
bwa = new BWAPairwiseAligner(ref_name, false);
}
// Produce aligned reads with variants called in parallel.
var reads = new BlockingCollection<Tuple<PacBioCCSRead, BWAPairwiseAlignment, List<Variant>>>();
Task producer = Task.Factory.StartNew(() =>
{
try
{
Parallel.ForEach(bamreader.Parse(bam_name), z => {
try {
BWAPairwiseAlignment aln = null;
List<Variant> variants = null;
if (callVariants) {
aln = bwa.AlignRead(z.Sequence) as BWAPairwiseAlignment;
if (aln!=null) {
variants = VariantCaller.CallVariants(aln);
variants.ForEach( p => {
p.StartPosition += aln.AlignedSAMSequence.Pos;
p.RefName = aln.Reference;
});
}
}
var res = new Tuple<PacBioCCSRead, BWAPairwiseAlignment, List<Variant>>(z, aln, variants);
reads.Add(res);
}
catch(Exception thrown) {
Console.WriteLine("CCS READ FAIL: " + z.Sequence.ID);
Console.WriteLine(thrown.Message);
} });
} catch(Exception thrown) {
Console.WriteLine("Could not parse BAM file: " + thrown.Message);
while(thrown.InnerException!=null) {
Console.WriteLine(thrown.InnerException.Message);
thrown = thrown.InnerException;
}
}
reads.CompleteAdding();
});
// Consume them into output files.
foreach(var r in reads.GetConsumingEnumerable()) {
foreach(var outputter in outputters) {
outputter.ConsumeCCSRead(r.Item1, r.Item2, r.Item3);
}
}
// throw any exceptions (this should be used after putting the consumer on a separate thread)
producer.Wait();
// Close the files
outputters.ForEach(z => z.Finish());
}
}
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 libbwasharp and libMonoPosixHelper" +
"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;
}
}
}
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;
}
}
}
public static void Main(string[] args)
{
try {
PlatformManager.Services.MaxSequenceSize = int.MaxValue;
PlatformManager.Services.DefaultBufferSize = 4096;
PlatformManager.Services.Is64BitProcessType = true;
if (args.Length > 3)
{
Console.WriteLine("Too many arguments");
DisplayHelp();
}
else if (args.Length < 2)
{
Console.WriteLine("Not enough arguments");
DisplayHelp();
}
else if (args [0] == "h" || args [0] == "help" || args [0] == "?" || args [0] == "-h")
{
DisplayHelp();
}
else
{
string bam_name = args [0];
string out_dir = args [1];
string ref_name = args.Length > 2 ? args [2] : null;
if (!File.Exists(bam_name))
{
Console.WriteLine("Can't find file: " + bam_name);
return;
}
if (ref_name != null && !File.Exists(ref_name))
{
Console.WriteLine("Can't find file: " + ref_name);
return;
}
if (Directory.Exists(out_dir))
{
Console.WriteLine("The output directory already exists, please specify a new directory or delete the old one.");
return;
}
Directory.CreateDirectory(out_dir);
List <CCSReadMetricsOutputter> outputters = new List <CCSReadMetricsOutputter> ()
{
new ZmwOutputFile(out_dir),
new ZScoreOutputter(out_dir),
new VariantOutputter(out_dir),
new SNROutputFile(out_dir),
new QVCalibration(out_dir)
};
ISequenceParser reader;
if (bam_name.EndsWith(".fastq", StringComparison.OrdinalIgnoreCase))
{
reader = new FastQCCSReader();
}
else
{
reader = new PacBioCCSBamReader();
}
BWAPairwiseAligner bwa = null;
bool callVariants = ref_name != null;
if (callVariants)
{
bwa = new BWAPairwiseAligner(ref_name, false);
}
// Produce aligned reads with variants called in parallel.
var reads = new BlockingCollection <Tuple <PacBioCCSRead, BWAPairwiseAlignment, List <Variant> > >();
Task producer = Task.Factory.StartNew(() =>
{
try
{
Parallel.ForEach(reader.Parse(bam_name), y => {
var z = y as PacBioCCSRead;
try {
BWAPairwiseAlignment aln = null;
List <Variant> variants = null;
if (callVariants)
{
aln = bwa.AlignRead(z.Sequence) as BWAPairwiseAlignment;
if (aln != null)
{
variants = VariantCaller.CallVariants(aln);
variants.ForEach(p => {
p.StartPosition += aln.AlignedSAMSequence.Pos;
p.RefName = aln.Reference;
});
}
}
var res = new Tuple <PacBioCCSRead, BWAPairwiseAlignment, List <Variant> >(z, aln, variants);
reads.Add(res);
}
catch (Exception thrown) {
Console.WriteLine("CCS READ FAIL: " + z.Sequence.ID);
Console.WriteLine(thrown.Message);
}
});
} catch (Exception thrown) {
Console.WriteLine("Could not parse BAM file: " + thrown.Message);
while (thrown.InnerException != null)
{
Console.WriteLine(thrown.InnerException.Message);
thrown = thrown.InnerException;
}
}
reads.CompleteAdding();
});
// Consume them into output files.
foreach (var r in reads.GetConsumingEnumerable())
{
foreach (var outputter in outputters)
{
outputter.ConsumeCCSRead(r.Item1, r.Item2, r.Item3);
}
}
// throw any exceptions (this should be used after putting the consumer on a separate thread)
producer.Wait();
// Close the files
outputters.ForEach(z => z.Finish());
}
}
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 libbwasharp and libMonoPosixHelper" +
"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;
}
}
}
