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/*++
Module Name:
AlignmentResult.h
Abstract:
Header for SNAP genome alignment results
Authors:
Bill Bolosky, May, 2014
Environment:
User mode service.
This class is NOT thread safe. It's the caller's responsibility to ensure that
at most one thread uses an instance at any time.
Revision History:
Pulled out of other places in SNAP
--*/
#pragma once
#include "Genome.h"
#include "directions.h"
class Read;
enum AlignmentResult {NotFound, SingleHit, MultipleHits, UnknownAlignment}; // BB: Changed Unknown to UnknownAlignment because of a conflict w/Windows headers
bool isAValidAlignmentResult(AlignmentResult result);
inline const char *AlignmentResultToString(AlignmentResult result) {
switch (result) {
case NotFound: return "NotFound";
case SingleHit: return "SingleHit";
case MultipleHits: return "MultipleHits";
case UnknownAlignment: return "Unknown";
default: return "Unknown alignment result type";
}
}
struct SingleAlignmentResult {
AlignmentResult status;
GenomeLocation location; // Aligned genome location.
Direction direction; // Did we match the reverse complement?
int score; // score of each end if matched
int scorePriorToClipping; // Score prior to soft clipping generated when a read aligns off the end of a contig
int mapq; // mapping quality, encoded like a Phred score (but as an integer, not ASCII Phred + 33).
int clippingForReadAdjustment;
bool usedAffineGapScoring;
int basesClippedBefore;
int basesClippedAfter;
int agScore;
bool supplementary;
static int compareByContigAndScore(const void *first, const void *second); // qsort()-style compare routine
static int compareByScore(const void *first, const void *second); // qsort()-style compare routine
};
// Does an AlignmentResult represent a single location?
inline bool isOneLocation(AlignmentResult result) {
return result == SingleHit;
}
const int NUM_READS_PER_PAIR = 2; // This is just to make it clear what the array subscripts are, it doesn't ever make sense to change
struct PairedAlignmentResult {
AlignmentResult status[NUM_READS_PER_PAIR]; // SingleHit or CertainHit if aligned, MultipleHit if matches DB
// but not confidently aligned, or NotFound.
GenomeLocation location[NUM_READS_PER_PAIR];// Genome location of each read.
GenomeLocation origLocation[NUM_READS_PER_PAIR]; // Genome location of each read prior to Landau-Vishkin adjustment
Direction direction[NUM_READS_PER_PAIR]; // Did we match the reverse complement? In general the two reads should have
// opposite orientations because they're part of the same original fragment,
// but it seems possible for a piece of the genome to get cut cleanly and flip
// in a translocation event, which would cause both ends of a fragment aligning
// there to be in the same orientation w.r.t. the reference genome.
int score[NUM_READS_PER_PAIR]; // score of each end if matched
int scorePriorToClipping[NUM_READS_PER_PAIR]; // Score prior to soft clipping generated when a read aligns off the end of a contig
int mapq[NUM_READS_PER_PAIR]; // mapping quality of each end, encoded like a Phred score (but as an integer, not ASCII Phred + 33).
int clippingForReadAdjustment[NUM_READS_PER_PAIR];
bool usedAffineGapScoring[NUM_READS_PER_PAIR];
int basesClippedBefore[NUM_READS_PER_PAIR];
int basesClippedAfter[NUM_READS_PER_PAIR];
int agScore[NUM_READS_PER_PAIR];
bool supplementary[NUM_READS_PER_PAIR];
int seedOffset[NUM_READS_PER_PAIR];
int lvIndels[NUM_READS_PER_PAIR];
double matchProbability[NUM_READS_PER_PAIR];
double probabilityAllPairs;
unsigned popularSeedsSkipped[NUM_READS_PER_PAIR];
bool alignedAsPair; // Were the reads aligned as a pair, or separately?
bool agForcedSingleAlignerCall; // Did we call the single aligner only because affine gap asked us to?
_int64 nanosInAlignTogether;
unsigned nLVCalls;
unsigned nSmallHits;
static int compareByContigAndScore(const void *first, const void *second); // qsort()-style compare routine
static int compareByScore(const void *first, const void *second); // qsort()-style compare routine
};
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