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// Author: Mark Chaisson
#pragma once
#include "BlasrHeaders.h"
//----------------------MODIFY ALIGNMENTS--------------------------//
//FIXME: refactor class SequenceIndexDatabase
void AssignRefContigLocation(T_AlignmentCandidate &alignment,
SequenceIndexDatabase<FASTQSequence> &seqdb, DNASequence &genome);
//FIXME: refactor class SequenceIndexDatabase
void AssignRefContigLocations(std::vector<T_AlignmentCandidate *> &alignmentPtrs,
SequenceIndexDatabase<FASTQSequence> &seqdb, DNASequence &genome);
template <typename T_RefSequence>
//FIXME: refactor class SequenceIndexDatabase
void AssignGenericRefContigName(std::vector<T_AlignmentCandidate *> &alignmentPtrs,
T_RefSequence &genome);
//FIXME: move to class ReadAlignments
void StoreRankingStats(std::vector<T_AlignmentCandidate *> &alignments,
VarianceAccumulator<float> &accumPValue,
VarianceAccumulator<float> &accumWeight);
//FIXME: mapQV should be assigned when alignments are created.
void AssignMapQV(std::vector<T_AlignmentCandidate *> &alignmentPtrs);
//FIXME: move to class ReadAlignments
void ScaleMapQVByClusterSize(T_AlignmentCandidate &alignment, MappingParameters ¶ms);
void StoreMapQVs(SMRTSequence &read, std::vector<T_AlignmentCandidate *> &alignmentPtrs,
MappingParameters ¶ms);
//--------------------SEARCH & CHECK ALIGNMENTS-------------------//
//FIXME: move to class ReadAlignments
template <typename T_Sequence>
bool CheckForSufficientMatch(T_Sequence &read, std::vector<T_AlignmentCandidate *> &alignmentPtrs,
MappingParameters ¶ms);
//FIXME: move to class ReadAlignments
int FindMaxLengthAlignment(std::vector<T_AlignmentCandidate *> alignmentPtrs, int &maxLengthIndex);
//FIXME: move to class T_AlignmentCandidate
void SumMismatches(SMRTSequence &read, T_AlignmentCandidate &alignment, int mismatchScore,
int fullIntvStart, int fullIntvEnd, MappingParameters ¶ms, int &sum);
//FIXME: move to class T_AlignmentCandidate
/// \returns whether two alignments overlap by more than minPcercentOverlap%
bool AlignmentsOverlap(T_AlignmentCandidate &alnA, T_AlignmentCandidate &alnB,
float minPercentOverlap);
/// \Partition overlapping alignments.
void PartitionOverlappingAlignments(std::vector<T_AlignmentCandidate *> &alignmentPtrs,
std::vector<std::set<int> > &partitions, float minOverlap);
//--------------------FILTER ALIGNMENTS---------------------------//
//FIXME: move to class T_AlignmentCandidate and ReadAlignments
int RemoveLowQualitySDPAlignments(int readLength,
std::vector<T_AlignmentCandidate *> &alignmentPtrs,
MappingParameters ¶ms);
//FIXME: move to class ReadAlignments
template <typename T_Sequence>
int RemoveLowQualityAlignments(T_Sequence &read, std::vector<T_AlignmentCandidate *> &alignmentPtrs,
MappingParameters ¶ms);
//FIXME: move to class ReadAlignments
int RemoveOverlappingAlignments(std::vector<T_AlignmentCandidate *> &alignmentPtrs,
MappingParameters ¶ms);
// FIXME: move to class ReadAlignments
// Delete all alignments from index startIndex in vector, inclusive.
void DeleteAlignments(std::vector<T_AlignmentCandidate *> &alignmentPtrs, int startIndex = 0);
//--------------------REFINE ALIGNMENTS---------------------------//
template <typename T_RefSequence, typename T_Sequence>
void RefineAlignment(std::vector<T_Sequence *> &bothQueryStrands, T_RefSequence &genome,
T_AlignmentCandidate &alignmentCandidate, MappingParameters ¶ms,
MappingBuffers &mappingBuffers);
template <typename T_RefSequence, typename T_Sequence>
void RefineAlignments(std::vector<T_Sequence *> &bothQueryStrands, T_RefSequence &genome,
std::vector<T_AlignmentCandidate *> &alignmentPtrs, MappingParameters ¶ms,
MappingBuffers &mappingBuffers);
//--------------------PRINT ALIGNMENTS---------------------------//
std::vector<T_AlignmentCandidate *> SelectAlignmentsToPrint(
std::vector<T_AlignmentCandidate *> alignmentPtrs, MappingParameters ¶ms,
const int &associatedRandInt);
//
// The full read is not the subread, and does not have masked off characters.
//
void PrintAlignment(T_AlignmentCandidate &alignment, SMRTSequence &fullRead,
MappingParameters ¶ms, AlignmentContext &alignmentContext,
std::ostream &outFile
#ifdef USE_PBBAM
,
SMRTSequence &subread, PacBio::BAM::IRecordWriter *bamWriterPtr
#endif
);
// Print all alignments in std::vector<T_AlignmentCandidate*> alignmentPtrs
void PrintAlignments(std::vector<T_AlignmentCandidate *> alignmentPtrs, SMRTSequence &read,
MappingParameters ¶ms, std::ostream &outFile,
AlignmentContext alignmentContext,
#ifdef USE_PBBAM
SMRTSequence &subread, PacBio::BAM::IRecordWriter *bamWriterPtr,
#endif
MappingSemaphores &semaphores);
void PrintAlignmentPtrs(std::vector<T_AlignmentCandidate *> &alignmentPtrs,
std::ostream &out = std::cout);
// Print an unaligned read, if noPrintUnalignedSeqs is True, print title only;
// otherwise, print title and sequence of the read.
void PrintUnaligned(const SMRTSequence &unalignedRead, std::ostream &unalignedFilePtr,
const bool noPrintUnalignedSeqs);
// Print all alignments for subreads in allReadAlignments.
// Input:
// allReadAlignments - contains a set of subreads, each of which
// is associated with a group of alignments.
// alignmentContext - an alignment context of each subread used
// for printing in SAM format.
// params - mapping parameters.
// Output:
// outFilePtr - where to print alignments for subreads.
// unalignedFilePtr - where to print sequences for unaligned subreads.
void PrintAllReadAlignments(ReadAlignments &allReadAlignments, AlignmentContext &alignmentContext,
std::ostream &outFilePtr, std::ostream &unalignedFilePtr,
MappingParameters ¶ms, std::vector<SMRTSequence> &subreads,
#ifdef USE_PBBAM
PacBio::BAM::IRecordWriter *bamWriterPtr,
#endif
MappingSemaphores &semaphores);
#include "BlasrUtilsImpl.hpp"
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