static Dictionary <string, int> highRepSeqs; // long seqs + counts for high depth reads
static void Main(string[] args)
{
if (args.Length == 0)
{
Console.WriteLine("FilterReadsByDepth -min minDepth -max maxDepth [-reduce maxCopies] [-histoOnly] [-stats statsFN] [-f format] [-t #threads] cbtFN fileNames");
return;
}
List <string> FNParams = new List <string>(); // the .cbt name and the set of file names or patterns
int noThreads = 2;
// find out who we are so we can track what program & args produced the result files
Process myProcess = Process.GetCurrentProcess();
myProcessNameAndArgs = myProcess.ProcessName;
foreach (string a in args)
{
myProcessNameAndArgs = myProcessNameAndArgs + " " + a;
}
for (int p = 0; p < args.Length; p++)
{
if (args[p][0] == '-')
{
args[p] = args[p].ToLower();
if (args[p] == "-s" || args[p] == "-stats")
{
if (!CheckForParamValue(p, args.Length, "stats file name string expected after -s|-stats"))
{
return;
}
statsFN = args[p + 1];
p++;
continue;
}
if (args[p] == "-min")
{
if (!CheckForParamValue(p, args.Length, "minDepth number expected after -min"))
{
return;
}
try
{
minDepth = Convert.ToInt32(args[p + 1]);
}
catch
{
Console.WriteLine("expected a number for the -min parameter: " + args[p + 1]);
return;
}
p++;
continue;
}
if (args[p] == "-max")
{
if (!CheckForParamValue(p, args.Length, "maxDepth number expected after -max"))
{
return;
}
try
{
maxDepth = Convert.ToInt32(args[p + 1]);
}
catch
{
Console.WriteLine("expected a number for the -max parameter: " + args[p + 1]);
return;
}
p++;
continue;
}
if (args[p] == "-r" || args[p] == "-reduce")
{
if (!CheckForParamValue(p, args.Length, "reduced depth number expected after -reduce"))
{
return;
}
try
{
reducedDepth = Convert.ToInt32(args[p + 1]);
reducingReads = true;
}
catch
{
Console.WriteLine("expected a number for the -reduce parameter: " + args[p + 1]);
return;
}
p++;
continue;
}
if (args[p] == "-histoonly" || args[p] == "-ho")
{
histoOnly = true;
continue;
}
if (args[p] == "-t" || args[p] == "-threads")
{
if (!CheckForParamValue(p, args.Length, "number expected after -t|-threads"))
{
return;
}
try
{
noThreads = Convert.ToInt32(args[p + 1]);
}
catch
{
Console.WriteLine("expected a number for the -t|-threads parameter: " + args[p + 1]);
return;
}
p++;
continue;
}
if (args[p] == "-f" || args[p] == "-format")
{
if (!CheckForParamValue(p, args.Length, "reads format expected after -f|-format"))
{
return;
}
string readsFormatParam = args[p + 1].ToLower();
if (readsFormatParam == "fna")
{
readsFormat = MerStrings.formatFNA;
}
else if (readsFormatParam == "fasta")
{
readsFormat = MerStrings.formatFNA;
}
else if (readsFormatParam == "fa")
{
readsFormat = MerStrings.formatFNA;
}
else if (readsFormatParam == "fastq")
{
readsFormat = MerStrings.formatFASTQ;
}
else if (readsFormatParam == "fq")
{
readsFormat = MerStrings.formatFASTQ;
}
else
{
Console.WriteLine("reads format must be fasta or fastq: " + args[p + 1]);
return;
}
p++;
continue;
}
if (args[p] == "-o" || args[p] == "-output")
{
if (!CheckForParamValue(p, args.Length, "directory name expected after -o|-output"))
{
return;
}
outputDir = args[p + 1];
p++;
continue;
}
}
FNParams.Add(args[p]);
}
if (FNParams.Count < 2)
{
Console.WriteLine("expected a cbt file name and at least one reads file name or pattern");
return;
}
// validate the output directory & set the output prefix string
string fnSeparator = Path.DirectorySeparatorChar.ToString(); // \ for Windows; / for Unix/Linux
if (outputDir != null)
{
try
{
// add a trailing \ if the output directory name doesn't already have one
if (!outputDir.EndsWith(fnSeparator))
{
outputDir += fnSeparator;
}
string testOutputFN = outputDir + "43EDD23F-5F68-47f0-B7B9-66AE9EE3BF0B.txt";
StreamWriter testTemp = new StreamWriter(testOutputFN);
testTemp.Close();
File.Delete(testOutputFN);
}
catch
{
Console.WriteLine("Output directory: " + args[6] + " was invalid");
return;
}
}
// take the cbt file name from the start of the non-option list
string cbtFN = FNParams[0];
FNParams.RemoveAt(0);
if (FNParams.Count == 0)
{
Console.WriteLine("did not find any reads file names or patterns");
return;
}
if (!File.Exists(cbtFN))
{
Console.WriteLine("k-mer consensus (.cbt) file not found: " + cbtFN);
return;
}
List <string> readsFileNames = new List <string>(FNParams.Count);
List <string> readsFilePaths = new List <string>(FNParams.Count);
foreach (string readsFNP in FNParams)
{
string readsFileName;
string readsFilePath;
GetPathFN(readsFNP, out readsFilePath, out readsFileName);
readsFilePaths.Add(readsFilePath);
readsFileNames.Add(readsFileName);
}
List <string> expandedReadsFNs = new List <string>();
for (int f = 0; f < FNParams.Count; f++)
{
string[] matchedReadsFNs = Directory.GetFiles(readsFilePaths[f], readsFileNames[f], SearchOption.TopDirectoryOnly);
foreach (string matchedReadsFN in matchedReadsFNs)
{
expandedReadsFNs.Add(matchedReadsFN);
}
}
// make sure there aren't any duplicates in the file list (seems to be a bug on the Cherax SGI HPC system and it returns each file name twice)
List <string> distinctReadsFNs = new List <string>();
foreach (string fn in expandedReadsFNs)
{
if (!distinctReadsFNs.Contains(fn))
{
distinctReadsFNs.Add(fn);
}
}
// finally... the set of fully qualified, distinct reads files
string[] readsFNs;
readsFNs = distinctReadsFNs.ToArray();
Array.Sort(readsFNs);
int noOfReadsFiles = distinctReadsFNs.Count;
if (noOfReadsFiles == 0)
{
Console.WriteLine("No matching reads files found");
return;
}
StreamReader formatTester = new StreamReader(readsFNs[0]);
string firstLine = formatTester.ReadLine();
if (firstLine[0] == '>')
{
readsFormat = MerStrings.formatFNA;
}
if (firstLine[0] == '@')
{
readsFormat = MerStrings.formatFASTQ;
}
formatTester.Close();
formatTester = null;
if (statsFN == null)
{
// construct a stats
statsFN = readsFileNames[0].Substring(0, readsFileNames[0].LastIndexOf('.'));
statsFN = statsFN.Replace('?', '_');
statsFN = statsFN.Replace('*', '_');
statsFN = statsFN.Replace('/', '_');
statsFN = statsFN.Replace('\\', '_');
statsFN = statsFN.Replace("__", "_");
statsFN = statsFN.Replace("__", "_");
statsFN = statsFN + "_fstats.txt";
statsFN = statsFN.Replace("__", "_");
}
// calculate the min load depth from the min reps depth - don't need to load all of the singletons and other errors into memory
//int minLoadDepth = minDepth / 2;
//if (minLoadDepth <= 1)
// minLoadDepth = 2;
int minLoadDepth = minDepth;
long loadedUniqueMers = 0;
long loadedTotalMers = 0;
// load the .cbt file into a merTable (either a hash table (small) or a sorted array (large))
long mersLoaded = MerStrings.LoadCBTFile(cbtFN, minLoadDepth, 0, 0, minDepth,
out uniqueMers, out merSize, out averageDepth, out loadedUniqueMers, out loadedTotalMers);
if (merSize < 1 || merSize > 32)
{
Console.WriteLine("bad k-mer size found at start of .cbt file");
return;
}
MerStrings.Initialise(merSize);
highRepSeqs = new Dictionary <string, int>(10000000);
highRepSeqs.Add(new string('A', 40), 0);
highRepSeqs.Add(new string('C', 40), 0);
highRepSeqs.Add(new string('G', 40), 0);
highRepSeqs.Add(new string('T', 40), 0);
// resolve the FASTQ qual ambiguity by reading through quals until one is encountered that can only come from either of the alternative sets
if (readsFormat == MerStrings.formatFASTQ)
{
qualBase = MerStrings.ResolveFastqQualAmbiguity(readsFNs[0], out fullQualHeaders);
}
// and check whether we've got Unix data so we can write out the corrected files in the same format
string lfConvention = MerStrings.LFConvention(readsFNs[0]);
// start the monitor/synchronising thread
Thread monitorProgress = new Thread(RateReporter);
monitorProgress.Priority = ThreadPriority.AboveNormal;
monitorProgress.Start();
readsFiles = new StreamReader[2];
filteredReads = new StreamWriter[2];
Dictionary <int, int> readDepths = new Dictionary <int, int>(1000);
// filter a pair of files at a time (allowing us to filter many files in a single run while keeping pairedness)
for (int f = 0; f < noOfReadsFiles; f += 2)
{
// for each file in the pair
for (int p = 0; p < 2; p++)
{
if (f + p < noOfReadsFiles)
{
string fullReadsFN = readsFNs[f + p];
string readsPath;
string readsFN;
GetPathFN(fullReadsFN, out readsPath, out readsFN);
string fileSuffix = readsFN.Substring(readsFN.LastIndexOf('.'));
string fileWithoutSuffix = readsFN.Substring(0, readsFN.LastIndexOf('.'));
readsFiles[p] = new StreamReader(fullReadsFN, Encoding.ASCII, false, 1000000);
Console.WriteLine("filtering " + readsFN);
// check that the file appears to be in the expected format
char firstChar = (char)readsFiles[p].Peek();
if (readsFormat == MerStrings.formatFASTQ && firstChar != '@')
{
Console.WriteLine(readsFN + " does not appear to be in FASTQ format");
return;
}
if (readsFormat == MerStrings.formatFNA && firstChar != '>')
{
Console.WriteLine(readsFN + " does not appear to be in FASTA format");
return;
}
string outputPath = outputDir == null ? readsPath + fnSeparator : outputDir;
if (!histoOnly)
{
string maxDepthString = maxDepth.ToString();
if (maxDepth == int.MaxValue)
{
maxDepthString = "max";
}
filteredReads[p] = new StreamWriter(outputPath + fileWithoutSuffix + "_" + minDepth + "_" + maxDepthString + fileSuffix,
false, readsFiles[p].CurrentEncoding, 1000000);
filteredReads[p].NewLine = lfConvention;
}
}
else
{
readsFiles[p] = null;
filteredReads[p] = null;
}
}
filterThreadParams[] filterParams = new filterThreadParams[noThreads];
Thread[] filteringThreads = new Thread[noThreads];
// ready a new thread for each parallel healer
for (int b = 0; b < noThreads; b++)
{
filterParams[b] = new filterThreadParams();
filterParams[b].threadNumber = b + 1;
filterParams[b].readsFiles = readsFiles;
filterParams[b].filteredReads = filteredReads;
filteringThreads[b] = new Thread(new ParameterizedThreadStart(Program.FilteringThread));
filteringThreads[b].Priority = ThreadPriority.BelowNormal;
filteringThreads[b].Name = b.ToString();
filteringThreads[b].Start(filterParams[b]);
}
// and wait for all threads to finish
for (int b = 0; b < noThreads; b++)
{
filteringThreads[b].Join();
filteringThreads[b] = null;
//Console.WriteLine("finished healing thread " + b);
}
foreach (StreamWriter r in filteredReads)
{
if (r != null)
{
r.Close();
}
}
// merge the per-thread histograms
for (int b = 0; b < noThreads; b++)
{
Dictionary <int, int> threadReadDepths = filterParams[b].depthHisto;
foreach (KeyValuePair <int, int> kvp in threadReadDepths)
{
if (readDepths.ContainsKey(kvp.Key))
{
readDepths[kvp.Key] += kvp.Value;
}
else
{
readDepths.Add(kvp.Key, kvp.Value);
}
}
}
} // for a pair of files
StreamWriter histo = new StreamWriter(statsFN);
histo.WriteLine(myProcessNameAndArgs);
histo.WriteLine();
histo.WriteLine("depth\tcount");
int[] depths = readDepths.Keys.ToArray <int>();
int[] counts = readDepths.Values.ToArray <int>();
Array.Sort <int, int>(depths, counts);
for (int i = 0; i < readDepths.Count; i++)
{
histo.WriteLine(depths[i] + "\t" + counts[i]);
}
Console.WriteLine("discarded " + reducedReads + "/" + discardedReads + " of " + totalReads + " reads");
histo.WriteLine("discarded " + reducedReads + "/" + discardedReads + " of " + totalReads + " reads");
histo.Close();
stopMonitor = true;
monitorProgress.Join();
}
private static void FilteringThread(object threadParams)
{
filterThreadParams theseParams = (filterThreadParams)threadParams;
int filterNumber = theseParams.threadNumber; // which healing thread is this one?
StreamReader[] readsFiles = theseParams.readsFiles; // the (shared) read files to be processed
StreamWriter[] filteredReads = theseParams.filteredReads; // corresponding (shared) streams for filtered reads
int noReadFNs = readsFiles.Length;
bool[] fileActive = new bool[noReadFNs]; // have not yet reached EOF on this reads file
bool[,] readValid = new bool[batchSize, noReadFNs]; // did the last read from this file produce a read?
int filesStillActive = 0; // how many active reads files are still around
string[,] readHeaderSet = new string[batchSize, noReadFNs]; // a batch of sets of read headers
string[,] readSet = new string[batchSize, noReadFNs]; // a batch of sets of reads, possibly one from each file
string[,] qualHeaderSet = new string[batchSize, noReadFNs]; //
string[,] qualsSet = new string[batchSize, noReadFNs]; // text form of the quals
int[] merDepths = new int[maxReadLength];
int[] depths = new int[noReadFNs]; // depths for each read in the set
bool[] rightDepth = new bool[noReadFNs]; // are depths within the requested bounds?
bool[] keepThisReadSet = new bool[batchSize]; // at least one of the set is of the desired depth, so keep the lot
Dictionary <int, int> readDepths = new Dictionary <int, int>(1000); // depth histogram for this thread
for (int f = 0; f < noReadFNs; f++)
{
if (readsFiles[f] != null)
{
fileActive[f] = true; // stays true until EOF
filesStillActive++;
}
}
// get the next set of reads and check their depths
while (filesStillActive > 0)
{
lock (readsFiles)
{
// try getting the next batch of reads
for (int b = 0; b < batchSize; b++)
{
for (int f = 0; f < noReadFNs; f++)
{
if (fileActive[f]) // only if we haven't already reached EOF on this file
{
readSet[b, f] = MerStrings.ReadRead(readsFiles[f], null, readsFormat, out readHeaderSet[b, f], out qualHeaderSet[b, f], out qualsSet[b, f]);
if (readSet[b, f] == null) // this read failed - now at EOF for the file
{
fileActive[f] = false;
readValid[b, f] = false;
filesStillActive--;
}
else
{
readValid[b, f] = true;
Interlocked.Increment(ref totalReads);
progressReads++;
}
}
else
{
readValid[b, f] = false;
}
}
}
} // lock to ensure synchronised reading from all reads files
// now have a set of reads (the n'th read from each file, if they exist. So filter each one in turn.
for (int b = 0; b < batchSize; b++)
{
keepThisReadSet[b] = true;
for (int f = 0; f < noReadFNs; f++)
{
if (readValid[b, f])
{
depths[f] = CalculateReadDepth(readSet[b, f], merDepths);
//if (depths[f] > 100000)
// Debugger.Break();
if (reducingReads && !histoOnly)
{
if (depths[f] >= minDepth) // possibly in the allowable range
{
if (depths[f] >= maxDepth) // above the max level, so a candidate for thinning
{
// extract and test all the long read keys
int keyReps = 0;
for (int i = 0; i < readSet[b, f].Length - 40; i++)
{
string readKey = readSet[b, f].Substring(i, 40);
// ignore them if they contain an N
if (readKey.Contains('N'))
{
continue;
}
// look the next seq in the table
if (highRepSeqs.ContainsKey(readKey))
{
highRepSeqs[readKey]++;
keyReps = highRepSeqs[readKey];
}
// and break if we found it
if (keyReps > 0)
{
break;
}
}
if (keyReps > reducedDepth)
{
rightDepth[f] = false; // we already have enough of these reads, so mark it to be discarded
Interlocked.Increment(ref reducedReads);
}
if (keyReps == 0) // didn't find this read already, so remember it for the future
{
string readKey = readSet[b, f].Substring(0, 40);
if (!readKey.Contains('N'))
{
lock (highRepSeqs)
{
if (!highRepSeqs.ContainsKey(readKey))
{
highRepSeqs.Add(readKey, 1);
}
}
}
rightDepth[f] = true; // and let the read through
}
}
else
{
rightDepth[f] = true; // reducing but read between min and max so let it through
}
}
else
{
rightDepth[f] = false; // reducing, but below the requested min depth
}
}
else
{
rightDepth[f] = depths[f] >= minDepth && depths[f] <= maxDepth; // not reducing, so must be between min and max
}
}
else
{
depths[f] = 0;
rightDepth[f] = false;
}
// keep the read only if all members of the set should be kept (if paired)
keepThisReadSet[b] = keepThisReadSet[b] & rightDepth[f];
if (readDepths.ContainsKey(depths[f]))
{
readDepths[depths[f]]++;
}
else
{
readDepths.Add(depths[f], 1);
}
}
} // end of checking a batch
for (int b = 0; b < batchSize; b++)
{
if (filesStillActive > 0 && !histoOnly)
{
lock (filteredReads)
{
for (int f = 0; f < noReadFNs; f++)
{
if (readValid[b, f])
{
if (keepThisReadSet[b])
{
SaveFilteredReadAndQual(filteredReads[f], readHeaderSet[b, f], readSet[b, f], qualsSet[b, f]);
progressWantedReads++;
}
else
{
Interlocked.Increment(ref discardedReads);
}
}
}
} // writing out a set of healed reads
}
}
} // end of file reading/healing loop
theseParams.depthHisto = readDepths;
}
