public int Extract(string sourceFile, string targetFile, IEnumerable <string> exceptQueryNames, string countFile)
{
int result = 0;
var except = new HashSet <string>(exceptQueryNames);
SmallRNACountMap cm = new SmallRNACountMap();
StreamWriter swCount = null;
if (File.Exists(countFile))
{
var oldCm = new SmallRNACountMap(countFile);
foreach (var c in oldCm.Counts)
{
cm.Counts[c.Key.StringBefore(SmallRNAConsts.NTA_TAG)] = c.Value;
}
swCount = new StreamWriter(targetFile + ".dupcount");
}
try
{
using (var sw = StreamUtils.GetWriter(targetFile, targetFile.ToLower().EndsWith(".gz")))
{
using (var sr = SAMFactory.GetReader(sourceFile, true))
{
string line;
var count = 0;
while ((line = sr.ReadLine()) != null)
{
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
var ss = SAMUtils.Parse <SAMItemSlim>(line);
ss.Qname = ss.Qname.StringBefore(SmallRNAConsts.NTA_TAG);
if (except.Contains(ss.Qname))
{
continue;
}
if (Filter != null && !Filter.Accept(ss))
{
continue;
}
except.Add(ss.Qname);
ss.WriteFastq(sw);
if (swCount != null)
{
swCount.WriteLine("{0}\t{1}", ss.Qname, cm.Counts[ss.Qname]);
}
result++;
}
}
}
}
finally
{
if (swCount != null)
{
swCount.Close();
}
}
return(result);
}
private static SAMItemSlim LineToSamItem(string line)
{
return(SAMUtils.Parse <SAMItemSlim>(line));
}