protected override void BeginProcessing()
{
Path = IO.GetAbsolutePath(this, Path);
if (AsEnumerator)
{
var reader = new StreamReader(Path, Encoding.UTF8);
var e = CTFTools.GetSampleReader(reader).GetEnumerator();
var psobj = new PSObject(e);
psobj.Properties.Add(new PSNoteProperty("Reader", reader));
WriteObject(psobj);
}
else
{
using (var reader = new StreamReader(Path, Encoding.UTF8))
{
var e = CTFTools.GetSampleReader(reader);
foreach (var sample in e)
{
WriteObject(sample);
if (sample.SequenceCount == ReadCount)
{
break;
}
}
}
}
}
private int GetTotalSeqCount()
{
if (_totalSeqCount != -1)
{
return(_totalSeqCount);
}
using (var reader = new StreamReader(Path, Encoding.UTF8))
{
_totalSeqCount = CTFTools.CountLines(reader).Item2;
return(_totalSeqCount);
}
}
protected override void BeginProcessing()
{
Path = IO.GetAbsolutePath(this, Path);
// Count sequeneces
Tuple <int, int> lines;
using (var reader = new StreamReader(Path, Encoding.UTF8))
{
lines = CTFTools.CountLines(reader);
}
WriteObject(new CTFLineInfo()
{
Lines = lines.Item1, Sequences = lines.Item2
});
}
protected override void BeginProcessing()
{
// Convert ratios into sequence counts
if (ParameterSetName == "ratios")
{
SequenceCounts = new int[Ratios.Length];
var total = GetTotalSeqCount();
for (var i = 0; i < Ratios.Length; ++i)
{
if (Ratios[i] == -1)
{
continue;
}
SequenceCounts[i] = (int)(Ratios[i] * total);
}
}
// Fix sequence counts
if (OutFiles.Length == SequenceCounts.Length)
{
var total = GetTotalSeqCount();
for (var i = 0; i < SequenceCounts.Length; ++i)
{
if (SequenceCounts[i] == -1)
{
SequenceCounts[i] = total - (SequenceCounts.Sum() + 1);
break;
}
}
}
else if (OutFiles.Length == SequenceCounts.Length + 1)
{
var lastCount = GetTotalSeqCount() - SequenceCounts.Sum();
var newSeqs = new int[SequenceCounts.Length + 1];
SequenceCounts.CopyTo(newSeqs, 0);
newSeqs[newSeqs.Length - 1] = lastCount;
SequenceCounts = newSeqs;
}
else
{
WriteError(new ErrorRecord(new ArgumentException("The number of SequenceCounts/Ratios should match the number of OutFiles"), "", ErrorCategory.InvalidArgument, null));
return;
}
for (var i = 0; i < SequenceCounts.Length; ++i)
{
WriteVerbose(string.Format("{0}-th sequences: {1}", i, SequenceCounts[i]));
}
// Get absolute paths
for (var i = 0; i < OutFiles.Length; ++i)
{
OutFiles[i] = IO.GetAbsolutePath(this, OutFiles[i]);
}
// Write partial files
using (var reader = new StreamReader(Path, Encoding.UTF8))
{
string lastLine = null;
for (var i = 0; i < OutFiles.Length; ++i)
{
using (var writer = new StreamWriter(OutFiles[i], false, new UTF8Encoding(false)))
{
lastLine = CTFTools.WritePartial(reader, writer, SequenceCounts[i], lastLine);
}
}
}
}
