public ExtractReadsTask(List <IReadPairHandler> pairHandlers, List <ReadPair> readPairs,
List <IBamWriterHandle> bamWriterHandles, IAlignmentPairFilter filter = null) : base()
{
_pairHandlers = pairHandlers;
_filter = filter;
_readPairs = readPairs;
_bamWriterHandles = bamWriterHandles;
}
public BamRewriter(IBamReader bamReader, IBamWriterMultithreaded bamWriter, IAlignmentPairFilter filter,
List <IReadPairHandler> pairHandlers, BlockingCollection <Task> taskQueue, bool getUnpaired = false, string chrFilter = null)
{
_bamReader = bamReader;
_bamWriter = bamWriter;
_filter = filter;
_pairHandlers = pairHandlers;
_getUnpaired = getUnpaired;
_chrFilter = chrFilter;
_taskQueue = taskQueue;
}
public BamRewriter(IBamReader bamReader, IBamWriter bamWriter, IAlignmentPairFilter filter,
IReadPairHandler pairHandler, long?bufferSize = 100000, bool getUnpaired = false, string chrFilter = null)
{
_bamReader = bamReader;
_bamWriter = bamWriter;
_filter = filter;
_pairHandler = pairHandler;
_bufferSize = bufferSize;
_getUnpaired = getUnpaired;
_chrFilter = chrFilter;
_alignmentBuffer = new List <BamAlignment>();
OnLog = message => Console.WriteLine(message);
}
public PairFilterReadPairSource(IBamReader bamReader, ReadStatusCounter readStatuses, bool skipAndRemoveDuplicates, IAlignmentPairFilter filter, int?refId = null,
int?expectedFragmentLength = null, bool filterForProperPairs = false)
{
_bamReader = bamReader;
_readStatuses = readStatuses;
_skipAndRemoveDuplicates = skipAndRemoveDuplicates;
if (refId != null)
{
_applyChrFilter = true;
_refId = refId.Value;
_bamReader.Jump(_refId, 0);
}
_filter = filter;
_filterForProperPairs = filterForProperPairs;
if (expectedFragmentLength != null)
{
_considerInsertSize = true;
_expectedFragmentLength = expectedFragmentLength.Value;
}
}
