private void AddAFile(string filepath)
{
if (SraCollection.Count == 0)
{
var theExtension = Path.GetExtension(filepath).ToLowerInvariant();
theExtension = theExtension == ".gz" ? Path.GetExtension(Path.GetFileNameWithoutExtension(filepath)).ToLowerInvariant() : theExtension;
switch (theExtension)
{
case ".fastq":
if (Path.GetFileName(filepath).Contains("_1") || Path.GetFileName(filepath).Contains("_2"))
{
RNASeqFastqDataGrid rnaSeqFastq = new RNASeqFastqDataGrid(filepath);
RnaSeqFastqCollection.Add(rnaSeqFastq);
UpdateOutputFolderTextbox();
break;
}
else
{
MessageBox.Show("FASTQ files must have *_1.fastq and *_2.fastq extensions.", "Run Workflows", MessageBoxButton.OK, MessageBoxImage.Information);
return;
}
}
}
else
{
MessageBox.Show("User already added SRA number. Please only choose one input: 1) SRA accession 2) FASTQ files.", "Run Workflows", MessageBoxButton.OK, MessageBoxImage.Information);
return;
}
}
private void AddAFile(string filepath)
{
var theExtension = Path.GetExtension(filepath).ToLowerInvariant();
string basepath = theExtension == ".gz" ? Path.GetFileNameWithoutExtension(Path.GetFileNameWithoutExtension(filepath)) : Path.GetFileNameWithoutExtension(filepath);
theExtension = theExtension == ".gz" ? Path.GetExtension(Path.GetFileNameWithoutExtension(filepath)).ToLowerInvariant() : theExtension;
switch (theExtension)
{
case ".fastq":
if (Path.GetFileName(basepath).EndsWith("_1") || Path.GetFileName(basepath).EndsWith("_2"))
{
bool isPairedEnd = Path.GetFileName(basepath).EndsWith("_2");
bool isUnpairedSecondMate = false;
bool isDifferentFolder = false;
foreach (var fq in RnaSeqFastqCollection)
{
bool hasMatePair = Path.GetFileName(fq.FileName.Substring(0, fq.FileName.Length - 2)) ==
Path.GetFileName(basepath.Substring(0, basepath.Length - 2));
if (hasMatePair)
{
fq.IsPairedEnd = true;
}
isPairedEnd = isPairedEnd || hasMatePair;
isUnpairedSecondMate = isUnpairedSecondMate || hasMatePair;
isDifferentFolder = isDifferentFolder ||
Path.GetDirectoryName(fq.FilePath) != Path.GetDirectoryName(filepath);
}
if (isDifferentFolder)
{
MessageBox.Show("All FASTQs must be located in the same analysis directory.", "Add FASTQ", MessageBoxButton.OK, MessageBoxImage.Warning);
}
else
{
RNASeqFastqDataGrid rnaSeqFastq = new RNASeqFastqDataGrid(filepath, isPairedEnd);
RnaSeqFastqCollection.Add(rnaSeqFastq);
UpdateOutputFolderTextbox();
}
break;
}
else
{
MessageBox.Show("FASTQ files must have *_1.fastq and/or *_2.fastq extensions.\n\n" +
"Single-end experiments must have unique filenames preceeding the *_1.fastq ending.\n\n" +
"Paired-end experiments must have the same unique filename preceeding the *_1.fastq and *_2.fastq suffixes.",
"Run Workflows", MessageBoxButton.OK, MessageBoxImage.Information);
return;
}
}
}