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 IDataSource <ReadPair> CreateReadPairSource(IBamReader bamReader, ReadStatusCounter statusCounter)
{
//var pairSourceLevelFilterProperPairs = _stitcherOptions.FilterForProperPairs;
var pairSourceLevelFilterProperPairs = false; // This gets taken care of at the Gemini level now.
var filter = new StitcherPairFilter(_stitcherOptions.FilterDuplicates,
pairSourceLevelFilterProperPairs, new AlignmentFlagDuplicateIdentifier(), statusCounter,
minMapQuality: 0, treatImproperAsIncomplete: false);
var readLength = 150;
return(new PairFilterReadPairSource(bamReader, statusCounter, _skipAndRemoveDuplicates,
filter, refId: _refId,
expectedFragmentLength: readLength, filterForProperPairs: pairSourceLevelFilterProperPairs));
}
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;
}
}