public void AppendStatusStringTag()
{
var counter = new ReadStatusCounter();
var handler = new DebugSummaryStatusHandler(counter);
var pair = TestHelpers.GetPair("10M", "10M");
pair.Read1.ReplaceOrAddStringTag("HI", "nothing");;
// Should not update
handler.AppendStatusStringTag("HI", "newvalue", pair.Read1);
Assert.Equal("nothing", pair.Read1.GetStringTag("HI"));
}
public void AddCombinedStatusStringTags()
{
var counter = new ReadStatusCounter();
var handler = new DebugSummaryStatusHandler(counter);
var pair = TestHelpers.GetPair("10M", "10M");
pair.Read1.ReplaceOrAddStringTag("HI", "read1_hi");
pair.Read2.ReplaceOrAddStringTag("HI", "read2_hi");
var outAlignment = new BamAlignment(pair.Read1);
outAlignment.ReplaceOrAddStringTag("HI", "nothing");
// Should not update
handler.AddCombinedStatusStringTags("HI", pair.Read1, pair.Read2, outAlignment);
Assert.Equal("nothing", outAlignment.GetStringTag("HI"));
}
public ReadPairRealignerAndCombiner GetRealignPairHandler(bool tryRestitch, bool alreadyStitched,
bool pairAwareRealign,
Dictionary <int, string> refIdMapping, ReadStatusCounter statusCounter, bool isSnowball,
IChromosomeIndelSource indelSource, string chromosome, Dictionary <string, IndelEvidence> masterLookup,
bool hasIndels, Dictionary <HashableIndel, int[]> outcomesLookup, bool skipRestitchIfNothingChanged)
{
var stitcher = GetStitcher();
var stitchedPairHandler = new PairHandler(refIdMapping, stitcher, tryStitch: tryRestitch);
var judger = new RealignmentJudger(GetAlignmentComparer());
var readRealigner = new GeminiReadRealigner(GetAlignmentComparer(), remaskSoftclips: _geminiOptions.RemaskMessySoftclips,
keepProbeSoftclips: _geminiOptions.KeepProbeSoftclip, keepBothSideSoftclips: _geminiOptions.KeepBothSideSoftclips || (_geminiOptions.KeepProbeSoftclip && alreadyStitched),
trackActualMismatches: _realignmentAssessmentOptions.TrackActualMismatches, checkSoftclipsForMismatches: _realignmentAssessmentOptions.CheckSoftclipsForMismatches,
debug: _geminiOptions.Debug, maskNsOnly: !(_geminiOptions.RemaskMessySoftclips || _geminiOptions.KeepProbeSoftclip || _geminiOptions.KeepBothSideSoftclips), maskPartialInsertion: _realignmentOptions.MaskPartialInsertion,
minimumUnanchoredInsertionLength: _realignmentOptions.MinimumUnanchoredInsertionLength,
minInsertionSizeToAllowMismatchingBases: 4, maxProportionInsertSequenceMismatch: 0.2); // TODO fix // TODO figure out what I was saying to fix here...
IStatusHandler statusHandler = new DebugSummaryStatusHandler(statusCounter);
if (_geminiOptions.Debug)
{
statusHandler = new DebugStatusHandler(statusCounter);
}
// Only softclip unknowns if it is not stitched to begin with (we believe in these more, plus it makes our lives simpler for dealing with stitched directions)
var softclipUnknownIndels = _geminiOptions.SoftclipUnknownIndels && !alreadyStitched;
//var regionFilterer = new RegionFilterer(chromosome, indelSource.Indels);
var regionFilterer = new DummyRegionFilterer();
var collector = GetCollector(isSnowball);
var realignmentEvaluator = new RealignmentEvaluator(indelSource.DeepCopy(), statusHandler, readRealigner, judger, chromosome,
_realignmentAssessmentOptions.TrackActualMismatches, _realignmentAssessmentOptions.CheckSoftclipsForMismatches, _geminiOptions.AllowRescoringOrigZero, softclipUnknownIndels,
regionFilterer, _geminiOptions.LightDebug);
return(new ReadPairRealignerAndCombiner(
collector,
GetRestitcher(stitchedPairHandler, statusHandler),
realignmentEvaluator,
GetIndelFinder(pairAwareRealign, chromosome, indelSource), chromosome, alreadyStitched, pairAwareRealign,
masterLookup: masterLookup, hasExistingIndels: hasIndels,
masterOutcomesLookup: outcomesLookup, skipRestitchIfNothingChanged: skipRestitchIfNothingChanged, allowedToStitch: !_geminiOptions.SkipStitching));
}
public void AddStatusCount()
{
var counter = new ReadStatusCounter();
var handler = new DebugSummaryStatusHandler(counter);
handler.AddStatusCount("x");
var statuses = counter.GetReadStatuses();
Assert.Equal(1.0, statuses.Count);
Assert.Equal(1, statuses["x"]);
handler.AddStatusCount("y");
statuses = counter.GetReadStatuses();
Assert.Equal(2, statuses.Count);
Assert.Equal(1, statuses["x"]);
Assert.Equal(1, statuses["y"]);
handler.AddStatusCount("x");
statuses = counter.GetReadStatuses();
Assert.Equal(2, statuses.Count);
Assert.Equal(2, statuses["x"]);
Assert.Equal(1, statuses["y"]);
}
