public RealignmentResult Realign(Read read, List <CandidateIndel> allTargets, string refSequence,
IIndelRanker ranker, HashSet <Tuple <string, string, string> > indelCandidateGroups = null, int maxIndelSize = 50)
{
try
{
// get targets near read
var readTargets = GetProximalTargets(read, allTargets, maxIndelSize);
ranker.Rank(readTargets);
var attempted = 0;
var result = GetBestAlignment(readTargets, read, refSequence, indelCandidateGroups, out attempted);
#if false
Console.WriteLine("{0}: Realigning {1} proximal targets, made {2} attempts. Best alignment has {3} mismatches {4} indels.",
read.Position, readTargets.Count(), attempted, result == null ? -1 : result.NumMismatches, result == null ? -1 : result.NumIndels);
#endif
return(result);
}
catch (Exception ex)
{
Logger.WriteExceptionToLog(new Exception(string.Format("Error aligning read '{0}'", read.Name), ex));
return(null);
}
}
public ChrRealigner(ChrReference chrReference, IAlignmentExtractor extractorForCandidates,
IAlignmentExtractor extractorForRealign, IIndelCandidateFinder indelFinder, IIndelRanker indelRanker,
ITargetCaller caller, RealignStateManager stateManager, IRealignmentWriter writer,
List <CandidateAllele> knownIndels = null, int maxIndelSize = 25, bool tryThree = false,
int anchorSizeThreshold = 10, bool skipDuplicates = false, bool skipAndRemoveDuplicates = false, bool remaskSoftclips = true, bool maskPartialInsertion = false, int minimumUnanchoredInsertionLength = 0,
bool tryRealignCleanSoftclippedReads = true, bool allowRescoringOrig0 = true, int maxRealignShift = 250, AlignmentScorer alignmentScorer = null, bool debug = false)
{
_chrReference = chrReference;
_extractorForCandidates = extractorForCandidates;
_extractorForRealign = extractorForRealign;
_indelFinder = indelFinder;
_indelRanker = indelRanker;
_caller = caller;
_stateManager = stateManager;
_writer = writer;
_knownIndels = knownIndels == null ? null : knownIndels.Select(i => new CandidateIndel(i)).ToList();
_maxIndelSize = maxIndelSize;
_anchorSizeThreshold = anchorSizeThreshold;
_skipDuplicates = skipDuplicates;
_skipAndRemoveDuplicates = skipAndRemoveDuplicates;
_allowRescoringOrig0 = allowRescoringOrig0;
_maxRealignShift = maxRealignShift;
_tryRealignCleanSoftclippedReads = tryRealignCleanSoftclippedReads;
_alignmentScorer = alignmentScorer;
_debug = debug;
if (alignmentScorer != null)
{
_alignmentComparer = new ScoredAlignmentComparer(alignmentScorer);
}
else
{
_alignmentComparer = new BasicAlignmentComparer();
}
_readRealigner = new ReadRealigner(_alignmentComparer, tryThree, remaskSoftclips, maskPartialInsertion, minimumUnanchoredInsertionLength);
}
