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;
}
}
}
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;
}
}
}