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/*++
Module Name:
Read.h
Abstract:
Headers for the Read class for the SNAP sequencer
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
Revision History:
Adapted from Matei Zaharia's Scala implementation.
--*/
#pragma once
#include "Compat.h"
#include "Tables.h"
#include "DataReader.h"
#include "DataWriter.h"
#include "directions.h"
#include "Error.h"
#include "Genome.h"
#include "AlignmentResult.h"
class FileFormat;
class Genome;
struct PairedAlignmentResult;
//#define LONG_READS
#ifdef LONG_READS
#define MAX_READ_LENGTH 400000
#else
#define MAX_READ_LENGTH 400
#endif
//
// Here's a brief description of the classes for input in SNAP:
// Read:
// A Read is some data that's come from a NGS machine. It includes some bases and associated quality score, as well as an ID.
// Reads may be clipped (because the sequencing machine was unsure of some bases). They may be switched between forward and
// reverse complement sense. They may or may not own their own memory for the various fields.
//
// ReadReader:
// A ReadReader understands how to generate reads from some input source (i.e., a FASTQ, SAM, BAM or CRAM file, for instance).
// It owns the storage for the read's information (i.e., the base string), but does not own the Read object itself. It is responsible
// for assuring that the memory for the read data is valid for the lifetime of the ReadReader (which, in practice, means it needs
// to use mapped files). ReadReaders may assume that they will only be called from one thread.
//
// PairedReadReader:
// Similar to a ReadReader, except that it gets mate pairs of Reads.
//
// ReadSupplier:
// A class that supplies reads to a consumer. It looks similar to a ReadReader, except that it own the storage for the
// ReadObject. The idea here is to allow the supplier to manage the memory that the Read object lives in so that a supplier
// can be implemented by a parallel queue with batches of reads in it. Supplier may, of course, also be implemented in
// different ways, such as range splitters. Like ReadReaders, ReadSuppliers will be called from only one thread. In
// practice, ReadSuppliers will have underlying ReadReaders (which might be behind a shared queue, for example).
//
// ReadSupplierGenerator:
// A class that creates a ReadSupplier. This has to be thread safe. The usual pattern is that the initialization code will
// create a read supplier generator, which will then be called on each of the threads to create a supplier, which will supply
// the reads to be aligned.
//
// PairedReadSupplierGenerator:
// The paired version of a ReadSupplier.
//
const int MaxReadLength = MAX_READ_LENGTH;
class Read;
enum ReadClippingType {NoClipping, ClipFront, ClipBack, ClipFrontAndBack};
struct ReaderContext
{
const Genome* genome;
const char* defaultReadGroup;
const char* defaultReadGroupAux; // SAM or BAM depending on output format
int defaultReadGroupAuxLen;
ReadClippingType clipping;
bool paired;
bool ignoreSecondaryAlignments; // Should we just ignore reads with the Secondary Alignment bit set?
bool ignoreSupplementaryAlignments; // Should we just ignore reads with the Supplementary Alignment bit set?
const char* header; // allocated buffer for header
size_t headerLength; // length of string
size_t headerBytes; // bytes used for header in file
bool headerMatchesIndex; // header refseq matches current index
char* rgLines;
size_t* rgLineOffsets;
int numRGLines;
};
class ReadReader {
public:
ReadReader(const ReaderContext& i_context) : context(i_context) {}
virtual ~ReadReader() {}
// reading
virtual bool getNextRead(Read *readToUpdate) = 0;
virtual void reinit(_int64 startingOffset, _int64 amountOfFileToProcess) = 0;
// if you keep a read after the next call to getNextRead, you must call holdBatch
// this increments the reference count to the batch
virtual void holdBatch(DataBatch batch) = 0;
// decremens hold refcount, when all holds are released the batch is no longer valid
virtual bool releaseBatch(DataBatch batch) = 0;
ReaderContext* getContext() { return &context; }
protected:
ReaderContext context;
};
class PairedReadReader {
public:
virtual ~PairedReadReader() {}
// reading
virtual bool getNextReadPair(Read *read1, Read *read2) = 0;
virtual void reinit(_int64 startingOffset, _int64 amountOfFileToProcess) = 0;
virtual void holdBatch(DataBatch batch) = 0;
virtual bool releaseBatch(DataBatch batch) = 0;
virtual ReaderContext* getContext() = 0;
// wrap a single read source with a matcher that buffers reads until their mate is found
static PairedReadReader* PairMatcher(ReadReader* single, bool quicklyDropUnpairedReads);
static const int MatchBuffers = 2;
};
class ReadSupplier {
public:
virtual Read *getNextRead() = 0; // This read is valid until you call getNextRead, then it's done. Don't worry about deallocating it.
virtual ~ReadSupplier() {}
virtual void holdBatch(DataBatch batch) = 0;
virtual bool releaseBatch(DataBatch batch) = 0;
};
class PairedReadSupplier {
public:
// These read are valid until you call getNextRead, then they're done. Don't worry about deallocating them.
virtual bool getNextReadPair(Read **read0, Read **read1) = 0;
virtual ~PairedReadSupplier() {}
virtual void holdBatch(DataBatch batch) = 0;
virtual bool releaseBatch(DataBatch batch) = 0;
};
class ReadSupplierGenerator {
public:
virtual ReadSupplier *generateNewReadSupplier() = 0;
virtual ReaderContext* getContext() = 0;
virtual ~ReadSupplierGenerator() {}
};
class PairedReadSupplierGenerator {
public:
virtual PairedReadSupplier *generateNewPairedReadSupplier() = 0;
virtual ReaderContext* getContext() = 0;
virtual ~PairedReadSupplierGenerator() {}
};
class ReadWriter {
public:
virtual ~ReadWriter() {}
// write out header
virtual bool writeHeader(const ReaderContext& context, bool sorted, int argc, const char **argv, const char *version, const char *rgLine, bool omitSQLines) = 0;
//
// write a batch of single reads, the first one of which is a primary alignment and the rest secondary.
//
virtual bool writeReads(const ReaderContext& context, Read *read, SingleAlignmentResult *results, _int64 nResults, bool firstIsPrimary, bool useAffineGap = false) = 0;
//
// Write a batch of paired alignments, including some single secondary alignments. reads needs to be exactly two reads, singleAlignmentResult is a pointer to two arrays of
// SingleAlignmentResults for single alignments of the respective reads, and the number of results is given by the two ints pointed to by nSingleResults. The first paired
// result is primary, all others are secondary.
//
virtual bool writePairs(const ReaderContext& context, Read **reads /* array of size 2 */, PairedAlignmentResult *result, _int64 nResults,
SingleAlignmentResult **singleResults /* array of size 2*/, _int64 *nSingleResults /* array of size 2*/, bool firstIsPrimary, bool useAffineGap = false) = 0;
// close out this thread
virtual void close() = 0;
};
class DataWriterSupplier;
class ReadWriterSupplier
{
public:
virtual ReadWriter* getWriter() = 0;
virtual void close() = 0;
static ReadWriterSupplier* create(const FileFormat* format, DataWriterSupplier* dataSupplier,
const Genome* genome, bool killIfTooSlowbool, bool emitInternalScore, char *internalScoreTag,
bool ignoreAlignmentAdjustmentsForOm);
};
#define READ_GROUP_FROM_AUX ((const char*) -1)
class Read {
public:
Read() :
id(NULL), data(NULL), quality(NULL),
localBufferAllocationOffset(0),
clippingState(NoClipping), currentReadDirection(FORWARD),
upcaseForwardRead(NULL), auxiliaryData(NULL), auxiliaryDataLength(0),
readGroup(NULL), library(NULL), libraryLength(0), originalAlignedLocation(-1), originalMAPQ(-1), originalSAMFlags(0),
originalFrontClipping(0), originalBackClipping(0), originalFrontHardClipping(0), originalBackHardClipping(0),
originalRNEXT(NULL), originalRNEXTLength(0), originalPNEXT(0), additionalFrontClipping(0), additionalBackClipping(0)
{}
Read(const Read& other) : localBufferAllocationOffset(0)
{
copyFromOtherRead(other);
}
~Read()
{
}
void dispose()
{
localBufferAllocationOffset = 0;
data = quality = unclippedData = unclippedQuality = externalData = NULL;
}
void operator=(const Read& other)
{
copyFromOtherRead(other);
}
void copyFromOtherRead(const Read& other)
{
id = other.id;
idLength = other.idLength;
frontClippedLength = other.frontClippedLength;
dataLength = other.dataLength;
externalData = other.externalData;
externalQuality = other.externalQuality;
currentReadDirection = other.currentReadDirection;
localBufferAllocationOffset = 0; // Clears out any allocations that might previously have been in the buffer
upcaseForwardRead = rcData = rcQuality = NULL;
unclippedLength = other.unclippedLength;
if (other.localBufferAllocationOffset != 0) {
//
// Copy the other read's local buffer to us.
//
assureLocalBufferLargeEnough();
_ASSERT(other.localBufferAllocationOffset <= localBufferLength);
memcpy(localBuffer, other.localBuffer, other.localBufferAllocationOffset);
localBufferAllocationOffset = other.localBufferAllocationOffset;
if (NULL != other.upcaseForwardRead) {
//
// Assert that it's in the other read's local buffer.
//
_ASSERT(other.upcaseForwardRead >= other.localBuffer && other.upcaseForwardRead <= other.localBuffer + other.localBufferAllocationOffset - unclippedLength);
//
// And put ours at the same offset in our local buffer.
//
upcaseForwardRead = localBuffer + (other.upcaseForwardRead - other.localBuffer);
}
if (NULL != other.rcData) {
//
// Assert that it's in the other read's local buffer.
//
_ASSERT(other.rcData >= other.localBuffer && other.rcData <= other.localBuffer + other.localBufferAllocationOffset - unclippedLength);
//
// And put ours at the same offset in our local buffer.
//
rcData = localBuffer + (other.rcData - other.localBuffer);
//
// And the same for RC quality.
//
_ASSERT(other.rcQuality >= other.localBuffer && other.rcQuality <= other.localBuffer + other.localBufferAllocationOffset - unclippedLength);
rcQuality = localBuffer + (other.rcQuality - other.localBuffer);
} else {
_ASSERT(NULL == other.rcQuality);
}
} else {
_ASSERT(other.upcaseForwardRead == NULL && other.rcData == NULL && other.rcQuality == NULL);
}
//
// Now set up the data, unclippedData, quality and unclippedQuality pointers.
//
if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
//
// Not in the other read's local buffer, so it must be external. Copy it.
//
data = other.data;
_ASSERT(NULL == other.localBuffer || other.quality < other.localBuffer || other.quality >= other.localBuffer + other.localBufferAllocationOffset);
quality = other.quality;
_ASSERT(NULL == other.localBuffer || other.unclippedData < other.localBuffer || other.unclippedData >= other.localBuffer + other.localBufferAllocationOffset);
unclippedData = other.unclippedData;
_ASSERT(NULL == other.localBuffer || other.unclippedQuality < other.localBuffer || other.unclippedQuality >= other.localBuffer + other.localBufferAllocationOffset);
unclippedQuality = other.unclippedQuality;
} else {
//
// It is in the other read's local buffer. Copy the local buffer offsets from the other read into this one.
//
data = localBuffer + (other.data - other.localBuffer);
_ASSERT(other.quality >= other.localBuffer && other.quality <= other.localBuffer + other.localBufferAllocationOffset - dataLength);
quality = localBuffer + (other.quality - other.localBuffer);
_ASSERT(other.unclippedData >= other.localBuffer && other.unclippedData <= other.localBuffer + other.localBufferAllocationOffset - unclippedLength);
unclippedData = localBuffer + (other.unclippedData - other.localBuffer);
_ASSERT(other.unclippedQuality >= other.localBuffer && other.unclippedQuality <= other.localBuffer + other.localBufferAllocationOffset - unclippedLength);
unclippedQuality = localBuffer + (other.unclippedQuality - other.localBuffer);
}
clippingState = other.clippingState;
batch = other.batch;
readGroup = other.readGroup;
library = other.library;
libraryLength = other.libraryLength;
auxiliaryData = other.auxiliaryData;
auxiliaryDataLength = other.auxiliaryDataLength;
originalAlignedLocation = other.originalAlignedLocation;
originalMAPQ = other.originalMAPQ;
originalSAMFlags = other.originalSAMFlags;
originalFrontClipping = other.originalFrontClipping;
originalBackClipping = other.originalBackClipping;
originalFrontHardClipping = other.originalFrontHardClipping;
originalBackHardClipping = other.originalBackHardClipping;
originalRNEXT = other.originalRNEXT;
originalRNEXTLength = other.originalRNEXTLength;
originalPNEXT = other.originalPNEXT;
additionalFrontClipping = other.additionalFrontClipping;
additionalBackClipping = other.additionalBackClipping;
}
//
// Initialize the Read. Reads do NOT take ownership of the memory to which they
// point, and it's the caller's responsibility to make sure that it continues to
// exist as long as the Read does. This is so that the caller can read a bunch of
// read data into a buffer, and then carve Reads out of it without doing further
// memory allocations, which would slow down the sequencing.
//
void init(
const char *i_id,
unsigned i_idLength,
const char *i_data,
const char *i_quality,
unsigned i_dataLength)
{
init(i_id, i_idLength, i_data, i_quality, i_dataLength, InvalidGenomeLocation, -1, 0, 0, 0, 0, 0, NULL, 0, 0);
}
void init(
const char * i_id,
unsigned i_idLength,
const char * i_data,
const char * i_quality,
unsigned i_dataLength,
GenomeLocation i_originalAlignedLocation,
unsigned i_originalMAPQ,
unsigned i_originalSAMFlags,
unsigned i_originalFrontClipping,
unsigned i_originalBackClipping,
unsigned i_originalFrontHardClipping,
unsigned i_originalBackHardClipping,
const char * i_originalRNEXT,
unsigned i_originalRNEXTLength,
unsigned i_originalPNEXT,
bool allUpper = false)
{
id = i_id;
idLength = i_idLength;
data = unclippedData = externalData = i_data;
quality = unclippedQuality = externalQuality = i_quality;
dataLength = i_dataLength;
unclippedLength = dataLength;
frontClippedLength = 0;
clippingState = NoClipping;
additionalFrontClipping = 0;
additionalBackClipping = 0;
originalAlignedLocation = i_originalAlignedLocation;
originalMAPQ = i_originalMAPQ;
originalSAMFlags = i_originalSAMFlags;
originalFrontClipping = i_originalFrontClipping;
originalBackClipping = i_originalBackClipping;
originalFrontHardClipping = i_originalFrontHardClipping;
originalBackHardClipping = i_originalBackHardClipping;
originalRNEXT = i_originalRNEXT;
originalRNEXTLength = i_originalRNEXTLength;
originalPNEXT = i_originalPNEXT;
currentReadDirection = FORWARD;
localBufferAllocationOffset = 0; // Clears out any allocations that might previously have been in the buffer
upcaseForwardRead = rcData = rcQuality = NULL;
//
// Check for lower case letters in the data, and convert to upper case if there are any. Also convert
// '.' to N.
//
if (! allUpper) {
unsigned anyLowerCase = 0;
for (unsigned i = 0; i < dataLength; i++) {
anyLowerCase |= IS_LOWER_CASE_OR_DOT[data[i]];
}
if (anyLowerCase) {
assureLocalBufferLargeEnough();
upcaseForwardRead = localBuffer;
localBufferAllocationOffset += unclippedLength;
for (unsigned i = 0; i < dataLength; i++) {
upcaseForwardRead[i] = TO_UPPER_CASE_DOT_TO_N[data[i]];
}
unclippedData = data = upcaseForwardRead;
//
// Quality must also be in localBuffer if data is. Copy it now.
//
memcpy(localBuffer + localBufferAllocationOffset, quality, unclippedLength);
unclippedQuality = quality = localBuffer + localBufferAllocationOffset;
localBufferAllocationOffset += unclippedLength;
}
}
}
// For efficiency, this class holds id, data and quality pointers that are
// *NOT* guaranteed to be to null-terminated strings; use the the length fields
// to figure out how far to read into these strings.
inline const char *getId() const {return id;}
inline unsigned getIdLength() const {return idLength;}
inline const char *getData() const {return data;}
inline const char *getUnclippedData() const {return unclippedData;}
inline const char *getQuality() const {return quality;}
inline const char *getUnclippedQuality() const {return unclippedQuality;}
inline unsigned getDataLength() const {return dataLength;}
inline unsigned getUnclippedLength() const {return unclippedLength;}
inline unsigned getFrontClippedLength() const {return (unsigned)(data - unclippedData);} // number of bases clipped from the front of the read
inline unsigned getBackClippedLength() const {return unclippedLength - dataLength - getFrontClippedLength();}
inline void setUnclippedLength(unsigned length) {unclippedLength = length;}
inline ReadClippingType getClippingState() const {return clippingState;}
inline DataBatch getBatch() { return batch; }
inline void setBatch(DataBatch b) { batch = b; }
inline const char* getReadGroup() const { return readGroup; }
inline void setReadGroup(const char* rg) { readGroup = rg; }
inline const char* getLibrary() const { return library; }
inline void setLibrary(const char* lb) { library = lb; }
inline int getLibraryLength() const { return libraryLength; }
inline void setLibraryLength(int length) { libraryLength = length; }
inline GenomeLocation getOriginalAlignedLocation() {return originalAlignedLocation;}
inline unsigned getOriginalMAPQ() {return originalMAPQ;}
inline unsigned getOriginalSAMFlags() {return originalSAMFlags;}
inline unsigned getOriginalFrontClipping() {return originalFrontClipping;}
inline unsigned getOriginalBackClipping() {return originalBackClipping;}
inline unsigned getOriginalFrontHardClipping() {return originalFrontHardClipping;}
inline unsigned getOriginalBackHardClipping() {return originalBackHardClipping;}
inline const char *getOriginalRNEXT() {return originalRNEXT;}
inline unsigned getOriginalRNEXTLength() {return originalRNEXTLength;}
inline unsigned getOriginalPNEXT() {return originalPNEXT;}
inline void addFrontClipping(int clipping) {
data += clipping;
dataLength -= clipping;
quality += clipping;
}
inline void setAdditionalFrontClipping(int clipping)
{
_ASSERT(0 <= clipping);
data += clipping - additionalFrontClipping;
dataLength -= clipping - additionalFrontClipping;
quality += clipping - additionalFrontClipping;
additionalFrontClipping = clipping;
}
inline void setAdditionalBackClipping(int clipping)
{
_ASSERT(0 <= clipping);
dataLength -= clipping - additionalBackClipping;
additionalBackClipping = clipping;
}
inline void addBackClipping(int clipping) {
dataLength -= clipping;
}
inline char* getAuxiliaryData(unsigned* o_length, bool * o_isSAM) const
{
*o_length = auxiliaryDataLength;
*o_isSAM = auxiliaryData && auxiliaryDataLength >= 5 && auxiliaryData[2] == ':';
return auxiliaryData;
}
inline void setAuxiliaryData(char* data, unsigned len)
{ auxiliaryData = data; auxiliaryDataLength = len; }
void clip(ReadClippingType clipping, bool maintainOriginalClipping = false) {
if (clipping == clippingState) {
//
// Already in the right state.
//
return;
}
//
// Revert to unclipped, then clip to the correct state.
//
dataLength = unclippedLength;
frontClippedLength = 0;
data = unclippedData;
quality = unclippedQuality;
//
// First clip from the back.
//
if (ClipBack == clipping || ClipFrontAndBack == clipping) {
unsigned backClipping = 0;
while (dataLength > 0 && quality[dataLength - 1] == '#') {
dataLength--;
backClipping++;
}
if (maintainOriginalClipping && backClipping < originalBackClipping) {
dataLength -= (originalBackClipping - backClipping);
}
}
//
// Then clip from the beginning.
//
if (ClipFront == clipping || ClipFrontAndBack == clipping) {
frontClippedLength = 0;
while (frontClippedLength < dataLength && quality[frontClippedLength] == '#') {
frontClippedLength++;
}
if (maintainOriginalClipping) {
frontClippedLength = max(frontClippedLength, originalFrontClipping);
}
}
_ASSERT(frontClippedLength <= dataLength);
dataLength -= frontClippedLength;
data += frontClippedLength;
quality += frontClippedLength;
clippingState = clipping;
};
unsigned countOfTrailing2sInQuality() const { // 2 here is represented in Phred+33, or ascii '#'
unsigned count = 0;
while (count < dataLength && quality[dataLength - 1 - count] == '#') {
count++;
}
return count;
}
unsigned countOfNs() const {
unsigned count = 0;
for (unsigned i = 0; i < dataLength; i++) {
count += IS_N[data[i]];
}
return count;
}
void computeReverseCompliment(char *outputBuffer) { // Caller guarantees that outputBuffer is at least getDataLength() bytes
for (unsigned i = 0; i < dataLength; i++) {
outputBuffer[i] = COMPLEMENT[data[dataLength - i - 1]];
}
}
void becomeRC()
{
if (RC == currentReadDirection) {
//
// We've already RCed ourself. Switch back.
//
if (NULL != upcaseForwardRead) {
unclippedData = upcaseForwardRead;
} else {
unclippedData = externalData;
}
unclippedQuality = externalQuality;
currentReadDirection = FORWARD;
} else {
if (rcData != NULL) {
//
// We've already been RC, just switch back.
//
unclippedData = rcData;
unclippedQuality = rcQuality;
} else {
assureLocalBufferLargeEnough();
rcData = localBuffer + localBufferAllocationOffset;
localBufferAllocationOffset += unclippedLength;
rcQuality = localBuffer + localBufferAllocationOffset;
localBufferAllocationOffset += unclippedLength;
_ASSERT(localBufferAllocationOffset <= localBufferLength);
for (unsigned i = 0; i < unclippedLength; i++) {
rcData[i] = COMPLEMENT[unclippedData[unclippedLength - i - 1]];
rcQuality[unclippedLength-i-1] = unclippedQuality[i];
}
unclippedData = rcData;
unclippedQuality = rcQuality;
}
currentReadDirection = RC;
}
//
// The clipping reverses as we go to/from RC.
//
frontClippedLength = unclippedLength - dataLength - frontClippedLength;
data = unclippedData + frontClippedLength;
quality = unclippedQuality + frontClippedLength;
unsigned temp = originalFrontClipping;
originalFrontClipping = originalBackClipping;
originalBackClipping = temp;
temp = originalFrontHardClipping;
originalFrontHardClipping = originalBackHardClipping;
originalBackHardClipping = temp;
}
static void checkIdMatch(Read* read0, Read* read1);
static void computeClippingFromCigar(const char *cigarBuffer, unsigned *originalFrontClipping, unsigned *originalBackClipping, unsigned *originalFrontHardClipping, unsigned *originalBackHardClipping)
{
size_t cigarSize;
const size_t cigarLimit = 1000;
for (cigarSize = 0; cigarSize < cigarLimit && cigarBuffer[cigarSize] != '\0' && cigarBuffer[cigarSize] != '\t'; cigarSize++) {
// This loop body intentionally left blank.
}
if (cigarSize == cigarLimit) {
WriteErrorMessage( "Absurdly long cigar string.\n");
soft_exit(1);
}
size_t frontHardClippingChars, backHardClippingChars, frontClippingChars, backClippingChars;
//
// Pull off the hard clipping first.
//
ExtractClipping(cigarBuffer, cigarSize, originalFrontHardClipping, originalBackHardClipping, 'H', &frontHardClippingChars, &backHardClippingChars);
_ASSERT(frontHardClippingChars + backHardClippingChars <= cigarSize);
//
// Now look at what's left of the cigar string to see if there's soft clipping.
//
ExtractClipping(cigarBuffer + frontHardClippingChars, cigarSize - frontHardClippingChars - backHardClippingChars, originalFrontClipping, originalBackClipping,
'S', &frontClippingChars, &backClippingChars);
}
private:
const char *id;
const char *data;
const char *unclippedData;
const char *unclippedQuality;
const char *quality;
const char *readGroup;
const char* library;
int libraryLength;
unsigned idLength;
unsigned dataLength;
unsigned unclippedLength;
unsigned frontClippedLength;
ReadClippingType clippingState;
int additionalFrontClipping;
int additionalBackClipping;
//
// Alignment data that was in the read when it was read from a file. While this should probably also be the place to put
// information that'll be used by the read writer, for now it's not. Hence, they're all called "original."
//
GenomeLocation originalAlignedLocation;
unsigned originalMAPQ;
unsigned originalSAMFlags;
unsigned originalFrontClipping;
unsigned originalBackClipping;
unsigned originalFrontHardClipping;
unsigned originalBackHardClipping;
const char *originalRNEXT;
unsigned originalRNEXTLength;
unsigned originalPNEXT;
//
// Memory that's local to this read and that is used to contain an upcased version of the read as well as
// RC read & quality strings. It survives init() so as to avoid memory allocation overhead.
//
char localBuffer[MAX_READ_LENGTH * 3];
static const unsigned localBufferLength;
unsigned localBufferAllocationOffset; // The next location to allocate in the local buffer.
char *upcaseForwardRead; // Either NULL or points into localBuffer. Used when the incoming read isn't all capitalized. Unclipped.
char *rcData; // Either NULL or points into localBuffer. Used when we've computed a reverse complement of the read, whether we're using it or not. Unclipped.
char *rcQuality; // Ditto for quality.
const char *externalData; // The data that was passed in at init() time, memory doesn't belong to this.
const char *externalQuality; // The quality that was passed in at init() time, memory doens't belong to this.
Direction currentReadDirection;
inline void assureLocalBufferLargeEnough()
{
#if 0 // Always true with static allocation
if (localBufferLength < 3 * unclippedLength) {
_ASSERT(0 == localBufferAllocationOffset); // Can only do this when the buffer is empty
if (NULL != localBuffer) {
BigDealloc(localBuffer);
}
localBufferLength = RoundUpToPageSize(3 * unclippedLength);
localBuffer = (char *)BigAlloc(localBufferLength);
}
#endif // 0
}
// batch for managing lifetime during input
DataBatch batch;
// auxiliary data in BAM or SAM format (can tell by looking at 3rd byte), if available
char* auxiliaryData;
unsigned auxiliaryDataLength;
//
// Pull the clipping info from the front and back of a cigar string.
static void ExtractClipping(const char *cigarBuffer, size_t cigarSize, unsigned *frontClipping, unsigned *backClipping, char clippingChar, size_t *frontClippingChars, size_t *backClippingChars)
{
*frontClipping = 0;
const size_t bufferSize = 20;
char buffer[bufferSize+1]; // +1 for trailing null
unsigned i;
for (i = 0; i < bufferSize && i < cigarSize && cigarBuffer[i] >= '0' && cigarBuffer[i] <= '9'; i++) {
buffer[i] = cigarBuffer[i];
}
if (cigarBuffer[i] == clippingChar) {
buffer[i] = '\0';
*frontClipping = atoi(buffer);
*frontClippingChars = i + 1;
} else {
*frontClippingChars = 0;
}
*backClipping = 0;
*backClippingChars = 0;
//
// Find the end of the cigar string by looking for either the end of the string or a tab. Just start where we
// were.
//
for (;i < cigarSize && cigarBuffer[i] != '\t' && cigarBuffer[i] != '\0'; i++) {
// This loop body intentionally left blank.
}
if (i > 1 && cigarBuffer[i-1] == clippingChar) {
for (i = i - 2; i >=0 && cigarBuffer[i] >= '0' && cigarBuffer[i] <= '9'; i--) {
// This loop body intentionally left blank.
}
//
// If we've gotten back to the beginning of the string, then the whole thing is one big soft clip. We arbitrarily
// select that to be front clipping, and so leave the back clipping alone.
if (i > 0) {
unsigned stringStart = i + 1;
for (i = stringStart; cigarBuffer[i] >= '0' && cigarBuffer[i] <= '9'; i++) {
buffer[i - stringStart] = cigarBuffer[i];
}
buffer[i - stringStart] = '\0';
*backClipping = atoi(buffer);
*backClippingChars = i - stringStart + 1;
}
}
}
};
//
// Reads that copy the memory for their strings. They're less efficient than the base
// Read class, but you can keep them around without holding references to the IO buffers
// and eventually stopping the IO.
//
class ReadWithOwnMemory : public Read {
public:
ReadWithOwnMemory() : Read(), extraBuffer(NULL), dataBuffer(NULL), idBuffer(NULL), qualityBuffer(NULL), auxBuffer(NULL) {}
ReadWithOwnMemory(const Read &baseRead) {
set(baseRead);
}
// must manually call destructor!
void dispose() {
if (extraBuffer != NULL) {
delete [] extraBuffer;
}
}
private:
void set(const Read &baseRead)
{
// allocate space in ownBuffer if possible; id/aux might need extraBuffer
dataBuffer = ownBuffer;
int ownBufferUsed = baseRead.getUnclippedLength() + 1;
qualityBuffer = ownBuffer + ownBufferUsed;
ownBufferUsed += baseRead.getUnclippedLength() + 1;
unsigned auxLen;
bool auxSam;
char* aux = baseRead.getAuxiliaryData(&auxLen, &auxSam);
if (baseRead.getIdLength() + 1 < sizeof(ownBuffer) - ownBufferUsed) {
idBuffer = ownBuffer + ownBufferUsed;
ownBufferUsed += baseRead.getIdLength() + 1;
} else {
idBuffer = NULL;
}
if (auxLen > 0 && auxLen < sizeof(ownBuffer) - ownBufferUsed) {
auxBuffer = ownBuffer + ownBufferUsed;
ownBufferUsed += auxLen;
} else {
auxBuffer = NULL;
}
if (idBuffer == NULL || (auxLen > 0 && auxBuffer == NULL)) {
extraBuffer = new char[(idBuffer == NULL ? baseRead.getIdLength() + 1 : 0) + auxLen];
int extraBufferUsed = 0;
if (idBuffer == NULL) {
idBuffer = extraBuffer;
extraBufferUsed += baseRead.getIdLength() + 1;
}
if (auxLen > 0 && auxBuffer == NULL) {
auxBuffer = extraBuffer + extraBufferUsed;
}
} else {
extraBuffer = NULL;
}
// copy data into buffers
memcpy(idBuffer,baseRead.getId(),baseRead.getIdLength());
idBuffer[baseRead.getIdLength()] = '\0'; // Even though it doesn't need to be null terminated, it seems like a good idea.
memcpy(dataBuffer,baseRead.getUnclippedData(),baseRead.getUnclippedLength());
dataBuffer[baseRead.getUnclippedLength()] = '\0';
memcpy(qualityBuffer,baseRead.getUnclippedQuality(),baseRead.getUnclippedLength());
qualityBuffer[baseRead.getUnclippedLength()] = '\0';
init(idBuffer,baseRead.getIdLength(),dataBuffer,qualityBuffer,baseRead.getUnclippedLength());
clip(baseRead.getClippingState());
setReadGroup(baseRead.getReadGroup());
setLibrary(baseRead.getLibrary());
setLibraryLength(baseRead.getLibraryLength());
if (aux != NULL && auxLen > 0) {
memcpy(auxBuffer, aux, auxLen);
setAuxiliaryData(auxBuffer, auxLen);
} else {
setAuxiliaryData(NULL, 0);
}
}
char ownBuffer[MAX_READ_LENGTH * 2 + 1000]; // internal buffer for copied data
char* extraBuffer; // extra buffer if internal buffer not big enough
// should all point into ownBuffer or extraBuffer
char *idBuffer;
char *dataBuffer;
char *qualityBuffer;
char *auxBuffer;
};
extern const unsigned DEFAULT_MIN_READ_LENGTH;
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