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/*++
Module Name:
PairedReadMatcher.cpp
Abstract:
Match paired-end reads coming in from different streams
Authors:
Bill Bolosky, November, 2012
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include <map>
#include "Compat.h"
#include "Util.h"
#include "Read.h"
#include "DataReader.h"
#include "VariableSizeMap.h"
#include "PairedEndAligner.h"
#include "SAM.h"
#include "Error.h"
// turn on to debug matching process
//#define VALIDATE_MATCH
// turn on to gather paired stats
//#define STATISTICS
using std::pair;
class PairedReadMatcher: public PairedReadReader
{
public:
PairedReadMatcher(ReadReader* i_single, bool i_quicklyDropUnpairedReads);
// PairedReadReader
virtual ~PairedReadMatcher();
virtual bool getNextReadPair(Read *read1, Read *read2);
virtual void reinit(_int64 startingOffset, _int64 amountOfFileToProcess)
{ single->reinit(startingOffset, amountOfFileToProcess); }
virtual void holdBatch(DataBatch batch)
{ single->holdBatch(batch); }
virtual bool releaseBatch(DataBatch batch);
virtual ReaderContext* getContext()
{ return single->getContext(); }
private:
ReadWithOwnMemory* allocOverflowRead();
void freeOverflowRead(ReadWithOwnMemory* read);
ReadReader* single; // reader for single reads
typedef _uint64 StringHash;
typedef VariableSizeMap<StringHash,Read> ReadMap;
DataBatch currentBatch; // for dropped reads
bool allDroppedInCurrentBatch;
DataBatch batch[2]; // 0 = current, 1 = previous
ReadMap unmatched[2]; // read id -> Read
typedef VariableSizeMap<PairedReadMatcher::StringHash,ReadWithOwnMemory*,150,MapNumericHash<PairedReadMatcher::StringHash>,80,0,true> OverflowMap;
OverflowMap overflow; // read id -> Read
typedef VariableSizeVector<ReadWithOwnMemory*> OverflowReadVector;
OverflowReadVector blocks; // BigAlloc blocks
static const int BlockSize = 10000; // # ReadWithOwnMemory per block
ExclusiveLock blockLock; // protects adding to blocks list
ReadWithOwnMemory* freeList; // head of free list, NULL if empty, use interlocked ops to update
typedef VariableSizeMap<_uint64,OverflowReadVector*> OverflowReadReleaseMap;
OverflowReadReleaseMap overflowRelease;
#ifdef VALIDATE_MATCH
typedef VariableSizeMap<StringHash,char*> StringMap;
StringMap strings;
typedef VariableSizeMap<StringHash,int> HashSet;
HashSet overflowUsed;
#endif
int overflowTotal, overflowPeak;
bool quicklyDropUnpairedReads;
_uint64 nReadsQuicklyDropped;
Read localRead;
#ifdef STATISTICS
typedef struct
{
_int64 oldPairs; // # pairs matched from overflow
_int64 oldBatches; // # distinct matches matched from overflow
_int64 internalPairs; // #pairs matched within batch
_int64 previousPairs; // #pairs matched with previous batch
_int64 overflowPairs; // #pairs left over
_int64 totalReads; // total reads in batch
void clear() { memset(this, 0, sizeof(*this)); }
} BatchStats;
BatchStats currentStats, totalStats;
VariableSizeMap<_int64,int> currentBatches;
#endif
};
PairedReadMatcher::PairedReadMatcher(
ReadReader* i_single,
bool i_quicklyDropUnpairedReads)
: single(i_single),
overflowTotal(0), overflowPeak(0),
quicklyDropUnpairedReads(i_quicklyDropUnpairedReads),
nReadsQuicklyDropped(0), freeList(NULL),
currentBatch(0, 0), allDroppedInCurrentBatch(false)
{
new (&unmatched[0]) VariableSizeMap<StringHash,Read>(10000);
new (&unmatched[1]) VariableSizeMap<StringHash,Read>(10000);
InitializeExclusiveLock(&blockLock);
#ifdef STATISTICS
currentStats.clear();
totalStats.clear();
#endif
}
PairedReadMatcher::~PairedReadMatcher()
{
for (OverflowReadVector::iterator i = blocks.begin(); i != blocks.end(); i++) {
BigDealloc(*i);
}
delete single;
DestroyExclusiveLock(&blockLock);
}
ReadWithOwnMemory*
PairedReadMatcher::allocOverflowRead()
{
while (true) {
ReadWithOwnMemory* next = freeList;
if (next == NULL) {
// alloc & init a new block of reads
ReadWithOwnMemory* block = (ReadWithOwnMemory*) BigAlloc(BlockSize * sizeof(ReadWithOwnMemory));
AcquireExclusiveLock(&blockLock);
blocks.push_back(block);
ReleaseExclusiveLock(&blockLock);
for (int i = 0; i < BlockSize - 1; i++) {
*(ReadWithOwnMemory**)&block[i] = &block[i+1];
}
while (true) {
ReadWithOwnMemory* head = freeList;
*(ReadWithOwnMemory**)&block[BlockSize-1] = head;
if (InterlockedCompareExchangePointerAndReturnOldValue((void*volatile*)&freeList, block, head) == head) {
break;
}
}
} else {
ReadWithOwnMemory* nextHead = *(ReadWithOwnMemory**)next;
if (InterlockedCompareExchangePointerAndReturnOldValue((void*volatile*)&freeList, nextHead, next) == next) {
return next;
}
}
}
}
void
PairedReadMatcher::freeOverflowRead(
ReadWithOwnMemory* read)
{
while (true) {
ReadWithOwnMemory* head = freeList;
*(ReadWithOwnMemory**)read = head;
if (InterlockedCompareExchangePointerAndReturnOldValue((void*volatile*)&freeList, read, head) == head) {
return;
}
}
}
bool
PairedReadMatcher::getNextReadPair(
Read *read1,
Read *read2)
{
Read *outputReads[NUM_READS_PER_PAIR];
outputReads[0] = read1;
outputReads[1] = read2;
int readOneToOutputRead; // This is used to determine which of the output reads corresponds to one (the read that just came from getNextRead())
// That, in turn, is determined by the S/BAM flags in the read saying whether it was first-in-template.
int skipped = 0;
while (true) {
if (skipped++ == 10000) {
WriteErrorMessage( "warning: no matching read pairs in 10,000 reads, input file might be unsorted or have unexpected read id format\n");
}
if (! single->getNextRead(&localRead)) {
#ifdef USE_DEVTEAM_OPTIONS
WriteErrorMessage("overflow total %d, peak %d\n", overflowTotal, overflowPeak);
#endif
int n = unmatched[0].size() + unmatched[1].size() + overflow.size();
if (n > 0) {
WriteErrorMessage( " warning: PairedReadMatcher discarding %d unpaired reads at eof\n", n);
#ifdef USE_DEVTEAM_OPTIONS
int printed = 0;
char buffer[200];
for (OverflowMap::iterator i = overflow.begin(); i != overflow.end() && printed < 10; i = overflow.next(i)) {
int l = min((unsigned) sizeof(buffer)-1, i->value->getIdLength());
memcpy(buffer, i->value->getId(), l);
buffer[l] = 0;
WriteErrorMessage("%s\n", buffer);
printed++;
}
#endif
#ifdef VALIDATE_MATCH
for (int i = 0; i < 2; i++) {
fprintf(stdout, "unmatched[%d]\n", i);
for (ReadMap::iterator j = unmatched[i].begin(); j != unmatched[i].end(); j = unmatched[i].next(j)) {
fprintf(stdout, "%s\n", strings[j->key]);
}
}
int printed = 0;
fprintf(stdout, "sample of overflow\n");
for (OverflowMap::iterator o = overflow.begin(); printed < 500 && o != overflow.end(); o = overflow.next(o)) {
if (NULL == overflowUsed.tryFind(o->key)) {
printed++;
fprintf(stdout, "%s\n", strings[o->key]);
}
}
#endif
}
if (nReadsQuicklyDropped > 0) {
WriteErrorMessage(" warning: PairedReadMatcher dropped %lld reads because they didn't have RNEXT and PNEXT filled in.\n"
" If your input file was generated by a single-end alignment (or this seems too big), use the -ku flag\n",
nReadsQuicklyDropped);
}
single->releaseBatch(batch[0]);
single->releaseBatch(batch[1]);
return false;
}
if (quicklyDropUnpairedReads) {
if (((localRead.getOriginalSAMFlags() & SAM_NEXT_UNMAPPED) == 0) && (localRead.getOriginalPNEXT() == 0 || (localRead.getOriginalRNEXTLength() == 1 && localRead.getOriginalRNEXT()[0] == '*'))) {
nReadsQuicklyDropped++;
skipped--;
continue;
}
}
if (localRead.getOriginalSAMFlags() & SAM_FIRST_SEGMENT) {
readOneToOutputRead = 0;
} else {
readOneToOutputRead = 1;
}
// build key for pending read table, removing /1 or /2 at end
const char* id = localRead.getId();
unsigned idLength = localRead.getIdLength();
// truncate at space or slash
char* slash = (char*) memchr((void*)id, '/', idLength);
if (slash != NULL) {
idLength = (unsigned)(slash - id);
}
char* space = (char*) memchr((void*)id, ' ', idLength);
if (space != NULL) {
idLength = (unsigned)(space - id);
}
StringHash key = util::hash64(id, idLength);
#ifdef VALIDATE_MATCH
char* s = new char[idLength+1];
memcpy(s, id, idLength);
s[idLength] = 0;
char** p = strings.tryFind(key);
if (p != NULL && strcmp(*p, s)) {
WriteErrorMessage( "hash collision %ld of %s and %s\n", key, *p, s);
soft_exit(1);
}
if (p == NULL) {
strings.put(key, s);
}
#endif
if (localRead.getBatch() != batch[0]) {
#ifdef STATISTICS
currentStats.oldBatches = currentBatches.size();
currentStats.overflowPairs = unmatched[1].size();
totalStats.internalPairs += currentStats.internalPairs;
totalStats.previousPairs += currentStats.previousPairs;
totalStats.oldBatches += currentStats.oldBatches;
totalStats.oldPairs += currentStats.oldPairs;
totalStats.overflowPairs += currentStats.overflowPairs;
totalStats.totalReads += currentStats.totalReads;
fprintf(stderr,"batch %d:%d: internal %d pairs, previous %d pairs, old %d pairs from %d batches, overflow %d pairs\n"
"cumulative: internal %d pairs, previous %d pairs, old %d pairs from %d batches, overflow %d pairs\n",
batch[0].fileID, batch[0].batchID, currentStats.internalPairs, currentStats.previousPairs, currentStats.oldPairs, currentStats.oldBatches, currentStats.overflowPairs,
totalStats.internalPairs, totalStats.previousPairs, totalStats.oldPairs, totalStats.oldBatches, totalStats.overflowPairs);
currentStats.clear();
currentBatches.clear();
#endif
// roll over batches
if (unmatched[1].size() > 0) {
// copy remaining reads into overflow map
//fprintf(stderr,"warning: PairedReadMatcher overflow %d unpaired reads from %d:%d\n", unmatched[1].size(), batch[1].fileID, batch[1].batchID); //!!
//char* buf = (char*) alloca(500);
for (ReadMap::iterator r = unmatched[1].begin(); r != unmatched[1].end(); r = unmatched[1].next(r)) {
ReadWithOwnMemory* p = allocOverflowRead();
new (p) ReadWithOwnMemory(r->value);
_ASSERT(p->getData()[0]);
overflow.put(r->key, p);
#ifdef VALIDATE_MATCH
char*s2 = *strings.tryFind(r->key);
int len = strlen(s2);
_ASSERT(! strncmp(s2, r->value.getId(), len));
ReadWithOwnMemory* rd = overflow.tryFind(r->key);
_ASSERT(! strncmp(s2, rd->getId(), len));
#endif
//memcpy(buf, r->value.getId(), r->value.getIdLength());
//buf[r->value.getIdLength()] = 0;
//fprintf(stderr, "overflow add %d:%d %s\n", batch[1].fileID, batch[1].batchID, buf);
}
overflowTotal += unmatched[1].size();
overflowPeak = max(overflow.size(), overflowPeak);
}
for (ReadMap::iterator i = unmatched[1].begin(); i != unmatched[1].end(); i = unmatched[1].next(i)) {
i->value.dispose();
}
unmatched[1].exchange(unmatched[0]);
unmatched[0].clear();
single->releaseBatch(batch[1]);
batch[1] = batch[0];
batch[0] = localRead.getBatch();
single->holdBatch(batch[0]);
#ifdef STATISTICS
currentStats.totalReads++;
#endif
}
ReadMap::iterator found = unmatched[0].find(key);
if (found != unmatched[0].end()) {
*outputReads[1-readOneToOutputRead] = found->value;
//fprintf(stderr, "current matched %d:%d->%d:%d %s\n", outputReads[1-readOneToOutputRead]->getBatch().fileID, outputReads[1-readOneToOutputRead]->getBatch().batchID, batch[0].fileID, batch[0].batchID, outputReads[1-readOneToOutputRead]->getId()); //!!
unmatched[0].erase(found->key);
#ifdef STATISTICS
currentStats.internalPairs++;
#endif
} else {
// try previous batch
found = unmatched[1].find(key);
if (found == unmatched[1].end()) {
// try overflow
OverflowMap::iterator found2 = overflow.find(key);
if (found2 == overflow.end()) {
// no match, remember it for later matching
unmatched[0].put(key, localRead);
_ASSERT(localRead.getData()[0] && unmatched[0][key].getData()[0]);
//fprintf(stderr, "unmatched add %d:%d %lx\n", batch[0].fileID, batch[0].batchID, key); //!!
continue;
} else {
// copy data into read, move from overflow table to release vector for current batch
found2->value->setBatch(batch[0]); // overwrite batch to match current
*outputReads[1-readOneToOutputRead] = * (Read*) found2->value;
_ASSERT(outputReads[1-readOneToOutputRead]->getData()[0]);
OverflowReadVector* v;
if (! overflowRelease.tryGet(batch[0].asKey(), &v)) {
v = new OverflowReadVector();
overflowRelease.put(batch[0].asKey(), v);
//fprintf(stderr,"overflow fetch into %d:%d\n", batch[0].fileID, batch[0].batchID);
}
v->push_back(found2->value);
overflow.erase(key);
//fprintf(stderr,"overflow matched %d:%d %s\n", read2->getBatch().fileID, read2->getBatch().batchID, read2->getId()); //!!
#ifdef VALIDATE_MATCH
overflowUsed.put(key, 1);
#endif
#ifdef STATISTICS
currentStats.oldPairs++;
currentBatches.put(read2->getBatch().asKey(), 1);
#endif
}
} else {
// found a match in preceding batch
*outputReads[1-readOneToOutputRead] = found->value;
//fprintf(stderr,"prior matched %d:%d->%d:%d %s\n", found->value.getBatch().fileID, found->gvalue.etBatch().batchID, batch[0].fileID, batch[0].batchID, found->value.getId()); //!!
unmatched[1].erase(found->key);
#ifdef STATISTICS
currentStats.previousPairs++;
#endif
}
}
// found a match
*outputReads[readOneToOutputRead] = localRead;
return true;
}
}
bool
PairedReadMatcher::releaseBatch(
DataBatch batch)
{
if (batch.asKey() == 0) {
return true;
} else if (single->releaseBatch(batch)) {
OverflowReadVector* v = NULL;
if (overflowRelease.tryGet(batch.asKey(), &v)) {
// free memory for overflow reads
//fprintf(stderr, "PairedReadMatcher release %d overflow reads for batch %d:%d\n", v->size(), batch.fileID, batch.batchID);
for (OverflowReadVector::iterator i = v->begin(); i != v->end(); i++) {
freeOverflowRead(*i);
}
delete v;
overflowRelease.erase(batch.asKey());
}
return true;
} else {
return false;
}
}
// define static factory function
PairedReadReader*
PairedReadReader::PairMatcher(
ReadReader* single,
bool quicklyDropUnpairedReads)
{
return new PairedReadMatcher(single, quicklyDropUnpairedReads);
}
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