private void VerifyBatchCandidates(ICandidateBatch batch, List <CandidateIndel> expected)
{
var candidates = batch.GetCandidates();
Assert.Equal(expected.Count, candidates.Count);
foreach (var candidate in candidates)
{
Assert.True(expected.Contains(candidate));
}
}
private void VerifyBatchContents(ICandidateBatch batch, List <CandidateAllele> expectedCandidates)
{
var candidates = batch.GetCandidates();
Assert.Equal(expectedCandidates.Count(), candidates.Count);
foreach (var expected in expectedCandidates)
{
Assert.True(candidates.Contains(expected));
}
}
public void AddMissingReferences(ICandidateBatch batch, List <Region> intervalsToAdd)
{
for (var i = 0; i < intervalsToAdd.Count; i++)
{
var interval = intervalsToAdd[i];
for (var position = interval.StartPosition; position <= interval.EndPosition; position++)
{
var refBase = _chrReference.GetBase(position);
batch.Add(new CandidateAllele(_chrReference.Name, position, refBase, refBase,
AlleleCategory.Reference));
}
}
}
public void DoneProcessing(ICandidateBatch batch)
{
var candidateBatch = batch as CandidateBatch;
if (candidateBatch != null)
{
foreach (var key in candidateBatch.BlockKeys)
{
var blockToRemove = _regionLookup[key];
_reusableBlocks.Push(blockToRemove); // save for reuse later
_regionLookup.Remove(key);
}
}
}
private void AddCollapsableFromOtherBlocks(ICandidateBatch batch, int maxClearedPosition, int upToPosition)
{
// grab all right anchored collapsable variants between max cleared and up to position and add to batch.
// this really only applies to snv/mnvs. collapsable insertions always have the same coordinate.
// if these variants dont collapse, they get added back to state manager later
foreach (var block in _regionLookup.Values)
{
if (block.StartPosition > maxClearedPosition && block.StartPosition <= upToPosition)
{
var collapsableVariants = block.ExtractCollapsable(upToPosition);
foreach (var collapsableVariant in collapsableVariants)
{
batch.Add(collapsableVariant);
}
}
}
}
public virtual void DoneProcessing(ICandidateBatch batch)
{
var candidateBatch = batch as CandidateBatch;
if (candidateBatch != null)
{
foreach (var key in candidateBatch.BlockKeys)
{
var blockToRemove = _regionLookup[key];
_reusableBlocks.Push(blockToRemove); // save for reuse later
_regionLookup.Remove(key);
if (_lastAccessedBlock != null && _lastAccessedBlock.Equals(blockToRemove))
{
_lastAccessedBlock = null;
}
}
}
}
public void Pad(ICandidateBatch batch, bool mapAll = false)
{
if (IntervalSet == null || (batch.ClearedRegions == null && !mapAll)) // nothing to do
{
return;
}
var startPosition = Math.Max(_lastClearedPosition + 1, IntervalSet.MinPosition);
var endPosition = mapAll ? IntervalSet.MaxPosition
: Math.Min(batch.ClearedRegions.Max(c => c.EndPosition), IntervalSet.MaxPosition);
if (startPosition > endPosition)
{
return;
}
var nonClearedIntervals = IntervalSet.GetClipped(new Region(startPosition, endPosition), batch.ClearedRegions);
AddMissingReferences(batch, nonClearedIntervals);
_lastClearedPosition = endPosition;
}
public override void DoneProcessing(ICandidateBatch batch)
{
var candidateBatch = batch as CandidateBatch;
if (batch.MaxClearedPosition.HasValue)
{
_lastMaxClearedPosition = batch.MaxClearedPosition.Value;
}
if (candidateBatch != null && candidateBatch.BlockKeys.Any())
{
var maxBlockKey = candidateBatch.BlockKeys.Max();
var keysToRemove = new List <int>();
foreach (var key in _regionLookup.Keys)
{
if (key < maxBlockKey) // want to only clear blocks outside of 1-block window for next potential batch
{
keysToRemove.Add(key);
}
}
foreach (var keyToRemove in keysToRemove)
{
var blockToRemove = _regionLookup[keyToRemove];
_reusableBlocks.Push(blockToRemove); // save for reuse later
_regionLookup.Remove(keyToRemove);
if (_lastAccessedBlock != null && _lastAccessedBlock.Equals(blockToRemove))
{
_lastAccessedBlock = null;
}
}
}
}
/// <summary>
/// Returns a list of called alleles, sorted by position, reference alternate
/// </summary>
/// <param name="batchToCall"></param>
/// <param name="source"></param>
/// <returns></returns>
public SortedList <int, List <CalledAllele> > Call(ICandidateBatch batchToCall, IAlleleSource source)
{
return(CallForPositions(batchToCall.GetCandidates(), source, batchToCall.MaxClearedPosition));
}
public IEnumerable <BaseCalledAllele> Call(ICandidateBatch batchToCall, IStateManager source)
{
return(CallForPositions(batchToCall.GetCandidates(), source, batchToCall.MaxClearedPosition));
}