533 lines
24 KiB
C++
533 lines
24 KiB
C++
|
||
#include "md_funcs.h"
|
||
|
||
#include <common/hts/bam_buf.h>
|
||
#include <common/utils/debug.h>
|
||
#include <common/utils/murmur3.h>
|
||
#include <common/utils/profiling.h>
|
||
#include <common/utils/timer.h>
|
||
#include <common/utils/util.h>
|
||
#include <sam/utils/read_ends.h>
|
||
#include <stdint.h>
|
||
|
||
#include <iostream>
|
||
#include <map>
|
||
#include <set>
|
||
#include <vector>
|
||
#include <math.h>
|
||
#include <unordered_map>
|
||
|
||
#include "dup_metrics.h"
|
||
#include "markdups_arg.h"
|
||
#include "shared_args.h"
|
||
|
||
using std::cerr;
|
||
using std::endl;
|
||
using std::map;
|
||
using std::set;
|
||
using std::unordered_map;
|
||
using std::vector;
|
||
|
||
/* 清除key位置的数据 */
|
||
void clearIdxAtPos(int64_t key, map<int64_t, set<int64_t>> *pmsIdx) {
|
||
auto &msIdx = *pmsIdx;
|
||
if (msIdx.find(key) != msIdx.end())
|
||
msIdx[key].clear(); // 清除该位点的冗余结果
|
||
}
|
||
|
||
/* 删除key位置的数据 */
|
||
void delIdxAtPos(int64_t key, map<int64_t, set<int64_t>> *pmsIdx) {
|
||
auto &msIdx = *pmsIdx;
|
||
if (msIdx.find(key) != msIdx.end())
|
||
msIdx.erase(key);
|
||
}
|
||
|
||
/*
|
||
* 计算read的分数
|
||
*/
|
||
int16_t computeDuplicateScore(BamWrap &bw) {
|
||
int16_t score = 0;
|
||
switch (g_mdArg.DUPLICATE_SCORING_STRATEGY) {
|
||
case ns_md::SUM_OF_BASE_QUALITIES:
|
||
// two (very) long reads worth of high-quality bases can go over
|
||
// Short.MAX_VALUE/2 and risk overflow.
|
||
score += (int16_t)min(bw.GetSumOfBaseQualities(), INT16_MAX / 2);
|
||
break;
|
||
case ns_md::TOTAL_MAPPED_REFERENCE_LENGTH:
|
||
if (!bw.GetReadUnmappedFlag())
|
||
// no need to remember the score since this scoring mechanism is
|
||
// symmetric
|
||
score = (int16_t)min(bw.GetReferenceLength(), INT16_MAX / 2);
|
||
break;
|
||
case ns_md::RANDOM:
|
||
// The RANDOM score gives the same score to both reads so that they get
|
||
// filtered together. it's not critical do use the readName since the
|
||
// scores from both ends get added, but it seem to be clearer this way.
|
||
score += (short)(Murmur3::Instance().HashUnencodedChars(bw.query_name()) & 0b11111111111111);
|
||
// subtract Short.MIN_VALUE/4 from it to end up with a number between
|
||
// 0 and Short.MAX_VALUE/2. This number can be then discounted in case
|
||
// the read is not passing filters. We need to stay far from overflow so
|
||
// that when we add the two scores from the two read mates we do not
|
||
// overflow since that could cause us to chose a failing read-pair
|
||
// instead of a passing one.
|
||
score -= INT16_MIN / 4;
|
||
default:
|
||
break;
|
||
}
|
||
// make sure that filter-failing records are heavily discounted. (the
|
||
// discount can happen twice, once for each mate, so need to make sure we do
|
||
// not subtract more than Short.MIN_VALUE overall.)
|
||
score += bw.GetReadFailsVendorQualityCheckFlag() ? (int16_t)(INT16_MIN / 2) : 0;
|
||
|
||
return score;
|
||
}
|
||
|
||
/*
|
||
* Builds a read ends object that represents a single read.
|
||
* 用来表示一个read的特征结构
|
||
*/
|
||
void buildReadEnds(BamWrap &bw, int64_t index, ReadNameParser &rnParser, ReadEnds *pKey) {
|
||
auto &k = *pKey;
|
||
auto &bc = bw.b->core;
|
||
k.read1FirstOfPair = bw.GetFirstOfPairFlag();
|
||
k.read1ReferenceIndex = bc.tid;
|
||
k.read1Coordinate = (bc.flag & BAM_FREVERSE) ? bw.GetUnclippedEnd() : bw.GetUnclippedStart();
|
||
k.orientation = (bc.flag & BAM_FREVERSE) ? ReadEnds::R : ReadEnds::F;
|
||
|
||
k.read1IndexInFile = index;
|
||
k.score = computeDuplicateScore(bw);
|
||
// Doing this lets the ends object know that it's part of a pair
|
||
if (bw.GetReadPairedFlag() && !bw.GetMateUnmappedFlag()) {
|
||
k.read2ReferenceIndex = bc.mtid;
|
||
}
|
||
// Fill in the location information for optical duplicates
|
||
rnParser.AddLocationInformation(bw.query_name(), pKey);
|
||
// cout << k.tile << ' ' << k.x << ' ' << k.y << endl;
|
||
// 计算位置key
|
||
k.posKey =
|
||
BamWrap::bam_global_pos(k.read1ReferenceIndex, k.read1Coordinate); // << 1 | k.orientation;
|
||
}
|
||
|
||
/**
|
||
* Takes a list of ReadEndsForMarkDuplicates objects and identify the
|
||
* representative read based on quality score. For all members of the duplicate
|
||
* set, add the read1 index-in-file of the representative read to the records of
|
||
* the first and second in a pair. This value becomes is used for the 'DI' tag.
|
||
*/
|
||
void addRepresentativeReadIndex(vector<const ReadEnds *> &vpRe) {}
|
||
|
||
/* 处理一组pairend的readends，标记冗余 */
|
||
void markDuplicatePairs(int64_t posKey, vector<const ReadEnds *> &vpRe,
|
||
DupContainer<int64_t> *dupIdx, DupContainer<int64_t> *opticalDupIdx) {
|
||
if (vpRe.size() < 2) {
|
||
if (vpRe.size() == 1) {
|
||
// addSingletonToCount(libraryIdGenerator);
|
||
}
|
||
return;
|
||
}
|
||
// cout << "pos:" << posKey + 1 << ";size:" << vpRe.size() << endl;
|
||
auto &vDupIdx = dupIdx->AtPos(posKey);
|
||
auto &vOpticalDupIdx = opticalDupIdx->AtPos(posKey);
|
||
|
||
int maxScore = 0;
|
||
const ReadEnds *pBest = nullptr;
|
||
/** All read ends should have orientation FF, FR, RF, or RR **/
|
||
for (auto pe : vpRe) // 找分数最高的readend
|
||
{
|
||
if (pe->score > maxScore || pBest == nullptr) {
|
||
maxScore = pe->score;
|
||
pBest = pe;
|
||
}
|
||
}
|
||
if (!g_mdArg.READ_NAME_REGEX.empty()) // 检查光学冗余
|
||
{
|
||
// trackOpticalDuplicates
|
||
}
|
||
for (auto pe : vpRe) // 对非best read标记冗余
|
||
{
|
||
if (pe != pBest) // 非best
|
||
{
|
||
vDupIdx.push_back(pe->read1IndexInFile); // 添加read1
|
||
if (pe->read2IndexInFile != pe->read1IndexInFile)
|
||
vDupIdx.push_back(pe->read2IndexInFile); // 添加read2
|
||
}
|
||
}
|
||
|
||
if (g_mdArg.TAG_DUPLICATE_SET_MEMBERS) {
|
||
addRepresentativeReadIndex(vpRe);
|
||
}
|
||
}
|
||
|
||
/* 处理一组非paired的readends，标记冗余 */
|
||
void markDuplicateFragments(int64_t posKey, vector<const ReadEnds *> &vpRe, bool containsPairs,
|
||
DupContainer<int64_t> *dupIdx) {
|
||
auto &vDupIdx = dupIdx->AtPos(posKey);
|
||
|
||
if (containsPairs) {
|
||
for (auto pe : vpRe) {
|
||
if (!pe->IsPaired()) {
|
||
vDupIdx.push_back(pe->read1IndexInFile);
|
||
}
|
||
}
|
||
} else {
|
||
int maxScore = 0;
|
||
const ReadEnds *pBest = nullptr;
|
||
for (auto pe : vpRe) {
|
||
if (pe->score > maxScore || pBest == nullptr) {
|
||
maxScore = pe->score;
|
||
pBest = pe;
|
||
}
|
||
}
|
||
|
||
for (auto pe : vpRe) {
|
||
if (pe != pBest) {
|
||
vDupIdx.push_back(pe->read1IndexInFile);
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/* 处理位于某个坐标的pairend reads */
|
||
void handlePairs(int64_t posKey, vector<ReadEnds> &readEnds,
|
||
vector<const ReadEnds *> &vpCache, DupContainer<int64_t> *dupIdx,
|
||
DupContainer<int64_t> *opticalDupIdx) {
|
||
if (readEnds.size() > 1) { // 有潜在的冗余
|
||
vpCache.clear();
|
||
// std::sort(readEnds.begin(), readEnds.end());
|
||
const ReadEnds *pReadEnd = nullptr;
|
||
for (auto &re : readEnds) {
|
||
if (pReadEnd != nullptr && ReadEnds::AreComparableForDuplicates(*pReadEnd, re, true)) // 跟前一个一样
|
||
vpCache.push_back(&re); // 处理一个潜在的冗余组
|
||
else {
|
||
markDuplicatePairs(posKey, vpCache, dupIdx,
|
||
opticalDupIdx); // 不一样
|
||
vpCache.clear();
|
||
vpCache.push_back(&re);
|
||
pReadEnd = &re;
|
||
}
|
||
}
|
||
markDuplicatePairs(posKey, vpCache, dupIdx, opticalDupIdx);
|
||
}
|
||
}
|
||
|
||
/* 处理位于某个坐标的 reads */
|
||
void handleFrags(int64_t posKey, vector<ReadEnds> &readEnds,
|
||
vector<const ReadEnds *> &vpCache, DupContainer<int64_t> *dupIdx) {
|
||
if (readEnds.size() > 1) // 有潜在的冗余
|
||
{
|
||
vpCache.clear();
|
||
// std::sort(readEnds.begin(), readEnds.end());
|
||
const ReadEnds *pReadEnd = nullptr;
|
||
bool containsPairs = false;
|
||
bool containsFrags = false;
|
||
for (auto &re : readEnds) {
|
||
if (pReadEnd != nullptr && ReadEnds::AreComparableForDuplicates(*pReadEnd, re, false)) {
|
||
vpCache.push_back(&re);
|
||
containsPairs = containsPairs || re.IsPaired();
|
||
containsFrags = containsFrags || !re.IsPaired();
|
||
} else {
|
||
if (vpCache.size() > 1 && containsFrags) {
|
||
markDuplicateFragments(posKey, vpCache, containsPairs, dupIdx);
|
||
}
|
||
vpCache.clear();
|
||
vpCache.push_back(&re);
|
||
pReadEnd = &re;
|
||
containsPairs = re.IsPaired();
|
||
containsFrags = !re.IsPaired();
|
||
}
|
||
}
|
||
if (vpCache.size() > 1 && containsFrags) {
|
||
markDuplicateFragments(posKey, vpCache, containsPairs, dupIdx);
|
||
}
|
||
}
|
||
}
|
||
|
||
/* 对找到的pairend read end添加一些信息 */
|
||
void modifyPairedEnds(const ReadEnds &fragEnd, ReadEnds *pPairedEnds) {
|
||
auto &pairedEnds = *pPairedEnds;
|
||
|
||
int64_t bamIdx = fragEnd.read1IndexInFile;
|
||
const int matesRefIndex = fragEnd.read1ReferenceIndex;
|
||
const int matesCoordinate = fragEnd.read1Coordinate;
|
||
// Set orientationForOpticalDuplicates, which always goes by the first then
|
||
// the second end for the strands. NB: must do this before updating the
|
||
// orientation later.
|
||
if (fragEnd.read1FirstOfPair) {
|
||
pairedEnds.orientationForOpticalDuplicates = ReadEnds::GetOrientationByte(
|
||
fragEnd.IsNegativeStrand(), pairedEnds.orientation == ReadEnds::R);
|
||
} else {
|
||
pairedEnds.orientationForOpticalDuplicates = ReadEnds::GetOrientationByte(
|
||
pairedEnds.orientation == ReadEnds::R, fragEnd.IsNegativeStrand());
|
||
}
|
||
// If the other read is actually later, simply add the other read's data as
|
||
// read2, else flip the reads
|
||
if (matesRefIndex > pairedEnds.read1ReferenceIndex ||
|
||
(matesRefIndex == pairedEnds.read1ReferenceIndex &&
|
||
matesCoordinate >= pairedEnds.read1Coordinate)) {
|
||
pairedEnds.read2ReferenceIndex = matesRefIndex;
|
||
pairedEnds.read2Coordinate = matesCoordinate;
|
||
pairedEnds.read2IndexInFile = bamIdx;
|
||
pairedEnds.orientation = ReadEnds::GetOrientationByte(pairedEnds.orientation == ReadEnds::R,
|
||
fragEnd.IsNegativeStrand());
|
||
|
||
// if the two read ends are in the same position, pointing in opposite
|
||
// directions, the orientation is undefined and the procedure above will
|
||
// depend on the order of the reads in the file. To avoid this, we set
|
||
// it explicitly (to FR):
|
||
if (pairedEnds.read2ReferenceIndex == pairedEnds.read1ReferenceIndex &&
|
||
pairedEnds.read2Coordinate == pairedEnds.read1Coordinate &&
|
||
pairedEnds.orientation == ReadEnds::RF) {
|
||
pairedEnds.orientation = ReadEnds::FR;
|
||
}
|
||
} else {
|
||
pairedEnds.read2ReferenceIndex = pairedEnds.read1ReferenceIndex;
|
||
pairedEnds.read2Coordinate = pairedEnds.read1Coordinate;
|
||
pairedEnds.read2IndexInFile = pairedEnds.read1IndexInFile;
|
||
pairedEnds.read1ReferenceIndex = matesRefIndex;
|
||
pairedEnds.read1Coordinate = matesCoordinate;
|
||
pairedEnds.read1IndexInFile = bamIdx;
|
||
pairedEnds.orientation = ReadEnds::GetOrientationByte(
|
||
fragEnd.IsNegativeStrand(), pairedEnds.orientation == ReadEnds::R);
|
||
pairedEnds.posKey = fragEnd.posKey;
|
||
}
|
||
pairedEnds.score += fragEnd.score;
|
||
}
|
||
|
||
static inline bool closeEnough(const ReadEnds *lhs, const ReadEnds *rhs, const int distance) {
|
||
return lhs != rhs && // no comparing an object to itself (checked using object identity)!
|
||
(lhs->tile != ReadEnds::NO_VALUE) &&
|
||
(rhs->tile != ReadEnds::NO_VALUE) && // no comparing objects without locations
|
||
lhs->tile == rhs->tile && // and the same tile
|
||
abs(lhs->x - rhs->x) <= distance && abs(lhs->y - rhs->y) <= distance;
|
||
}
|
||
|
||
static inline bool closeEnoughShort(const ReadEnds *lhs, const ReadEnds *rhs, const int distance) {
|
||
return lhs != rhs && abs(lhs->x - rhs->x) <= distance && abs(lhs->y - rhs->y) <= distance;
|
||
}
|
||
|
||
/**
|
||
* Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of
|
||
* one another. Within each cluster of optical duplicates that is found, one read remains un-flagged for
|
||
* optical duplication and the rest are flagged as optical duplicates. The set of reads that are considered
|
||
* optical duplicates are indicated by returning "true" at the same index in the resulting boolean[] as the
|
||
* read appeared in the input list of physical locations.
|
||
*
|
||
* @param list a list of reads that are determined to be duplicates of one another
|
||
* @param keeper a single PhysicalLocation that is the one being kept as non-duplicate, and thus should never be
|
||
* annotated as an optical duplicate. May in some cases be null, or a PhysicalLocation not
|
||
* contained within the list! (always not be null!)
|
||
* @return a boolean[] of the same length as the incoming list marking which reads are optical duplicates
|
||
*/
|
||
static void findOpticalDuplicates(vector<const ReadEnds *> &readEndsArr, const ReadEnds *pBestRe,
|
||
vector<bool> *pOpticalDuplicateFlags) {
|
||
const int DEFAULT_OPTICAL_DUPLICATE_DISTANCE = 100;
|
||
const int DEFAULT_MAX_DUPLICATE_SET_SIZE = 300000;
|
||
|
||
vector<bool> &opticalDuplicateFlags = *pOpticalDuplicateFlags;
|
||
// opticalDuplicateFlags.push_back(true); // for test
|
||
int len = readEndsArr.size();
|
||
// If there is only one or zero reads passed in (so there are obviously no optical duplicates),
|
||
// or if there are too many reads (so we don't want to try to run this expensive n^2 algorithm),
|
||
// then just return an array of all false
|
||
if (len < 2 || len > DEFAULT_MAX_DUPLICATE_SET_SIZE) {
|
||
return;
|
||
}
|
||
|
||
if (len >= 4) {
|
||
/**
|
||
* Compute the optical duplicates correctly in the case where the duplicate group could end up with transitive
|
||
* optical duplicates
|
||
* getOpticalDuplicatesFlagWithGraph
|
||
*/
|
||
// Make a graph where the edges are reads that lie within the optical duplicate pixel distance from each other,
|
||
// we will then use the union-find algorithm to cluster the graph and find optical duplicate groups
|
||
Graph<int> opticalDistanceRelationGraph;
|
||
unordered_map<int, vector<int>> tileRGmap;
|
||
int keeperIndex = -1;
|
||
for (int i = 0; i < readEndsArr.size(); ++i) {
|
||
const ReadEnds *currentLoc = readEndsArr[i];
|
||
if (currentLoc == pBestRe)
|
||
keeperIndex = i;
|
||
if (currentLoc->tile != ReadEnds::NO_VALUE) {
|
||
int key = currentLoc->tile; // 只处理一个样本，所以只有一个read group
|
||
tileRGmap[key].push_back(i);
|
||
}
|
||
opticalDistanceRelationGraph.addNode(i);
|
||
}
|
||
// Since because finding adjacent optical duplicates is an O(n^2) operation, we can subdivide the input into its
|
||
// readgroups in order to reduce the amount of redundant checks across readgroups between reads.
|
||
// fillGraphFromAGroup
|
||
for (auto &entry : tileRGmap) {
|
||
auto &groupList = entry.second;
|
||
if (groupList.size() > 1) {
|
||
for (int i = 0; i < groupList.size(); ++i) {
|
||
int iIndex = groupList[i];
|
||
const ReadEnds *currentLoc = readEndsArr[iIndex];
|
||
for (int j = i + 1; j < groupList.size(); ++j) {
|
||
int jIndex = groupList[j];
|
||
const ReadEnds *other = readEndsArr[jIndex];
|
||
if (closeEnoughShort(currentLoc, other, DEFAULT_OPTICAL_DUPLICATE_DISTANCE))
|
||
opticalDistanceRelationGraph.addEdge(iIndex, jIndex);
|
||
}
|
||
}
|
||
}
|
||
}
|
||
// Keep a map of the reads and their cluster assignments
|
||
unordered_map<int, int> opticalDuplicateClusterMap;
|
||
opticalDistanceRelationGraph.cluster(&opticalDuplicateClusterMap);
|
||
unordered_map<int, int> clusterToRepresentativeRead;
|
||
int keeperCluster = -1;
|
||
// Specially mark the keeper as specifically not a duplicate if it exists
|
||
if (keeperIndex >= 0) {
|
||
keeperCluster = opticalDuplicateClusterMap[keeperIndex];
|
||
clusterToRepresentativeRead[keeperCluster] = keeperIndex;
|
||
}
|
||
|
||
for (auto &entry: opticalDuplicateClusterMap) {
|
||
int recordIndex = entry.first;
|
||
int recordAssignedCluster = entry.second;
|
||
// If its not the first read we've seen for this cluster, mark it as an optical duplicate
|
||
auto repReadItr = clusterToRepresentativeRead.find(recordAssignedCluster);
|
||
if (repReadItr != clusterToRepresentativeRead.end() && recordIndex != keeperIndex) {
|
||
const ReadEnds *representativeLoc = readEndsArr[repReadItr->second];
|
||
const ReadEnds *currentRecordLoc = readEndsArr[recordIndex];
|
||
// If not in the keeper cluster, then keep the minX -> minY valued duplicate (note the tile must be
|
||
// equal for reads to cluster together)
|
||
if (!(keeperIndex >= 0 && recordAssignedCluster == keeperCluster) &&
|
||
(currentRecordLoc->x < representativeLoc->x ||
|
||
(currentRecordLoc->x == representativeLoc->x && currentRecordLoc->y < representativeLoc->y))) {
|
||
// Mark the old min as an optical duplicate, and save the new min
|
||
opticalDuplicateFlags[repReadItr->second] = true;
|
||
clusterToRepresentativeRead[recordAssignedCluster] = recordIndex;
|
||
} else {
|
||
// If a smaller read has already been visited, mark the test read as an optical duplicate
|
||
opticalDuplicateFlags[recordIndex] = true;
|
||
}
|
||
} else {
|
||
clusterToRepresentativeRead[recordAssignedCluster] = recordIndex;
|
||
}
|
||
}
|
||
} else {
|
||
/**
|
||
* Compute optical duplicates quickly in the standard case where we know that there won't be any transitive
|
||
* distances to worry about. Note, this is guaranteed to be correct when there are at most 2x reads from a
|
||
* readgroup or 3x with the keeper present
|
||
* getOpticalDuplicatesFlagFast
|
||
*/
|
||
// First go through and compare all the reads to the keeper
|
||
for (int i = 0; i < len; ++i) {
|
||
const ReadEnds *other = readEndsArr[i];
|
||
opticalDuplicateFlags[i] = closeEnough(pBestRe, other, DEFAULT_OPTICAL_DUPLICATE_DISTANCE);
|
||
}
|
||
// Now go through and do each pairwise comparison not involving the actualKeeper
|
||
for (int i = 0; i < len; ++i) {
|
||
const ReadEnds *lhs = readEndsArr[i];
|
||
if (lhs == pBestRe) // no comparisons to actualKeeper since those are all handled above
|
||
continue;
|
||
for (int j = i + 1; j < len; ++j) {
|
||
const ReadEnds *rhs = readEndsArr[j];
|
||
if (rhs == pBestRe) // no comparisons to actualKeeper since those are all handled above
|
||
continue;
|
||
if (opticalDuplicateFlags[i] && opticalDuplicateFlags[j])
|
||
continue; // both already marked, no need to check
|
||
if (closeEnough(lhs, rhs, DEFAULT_OPTICAL_DUPLICATE_DISTANCE)) {
|
||
// At this point we want to mark either lhs or rhs as duplicate. Either could have been marked
|
||
// as a duplicate of the keeper (but not both - that's checked above), so be careful about which
|
||
// one to now mark as a duplicate.
|
||
int index = opticalDuplicateFlags[j] ? i : j;
|
||
opticalDuplicateFlags[index] = true;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/**
|
||
* Looks through the set of reads and identifies how many of the duplicates are
|
||
* in fact optical duplicates, and stores the data in the instance level histogram.
|
||
*
|
||
* We expect only reads with FR or RF orientations, not a mixture of both.
|
||
*
|
||
* In PCR duplicate detection, a duplicates can be a have FR and RF when fixing the orientation order to the first end
|
||
* of the mate. In optical duplicate detection, we do not consider them duplicates if one read as FR and the other RF
|
||
* when we order orientation by the first mate sequenced (read #1 of the pair).
|
||
*/
|
||
static int checkOpticalDuplicates(vector<const ReadEnds *> &readEndsArr, const ReadEnds *pBestRe) {
|
||
vector<bool> opticalDuplicateFlags(readEndsArr.size(), false);
|
||
// find OpticalDuplicates
|
||
findOpticalDuplicates(readEndsArr, pBestRe, &opticalDuplicateFlags);
|
||
int opticalDuplicates = 0;
|
||
for (int i = 0; i < opticalDuplicateFlags.size(); ++i) {
|
||
ReadEnds *pRe = const_cast<ReadEnds *>(readEndsArr[i]);
|
||
if (opticalDuplicateFlags[i]) {
|
||
++opticalDuplicates;
|
||
// if (zzhopticalSet.find(pRe->read1IndexInFile) != zzhopticalSet.end()) {
|
||
// cout << "val: " << pRe->isOpticalDuplicate << endl;
|
||
// }
|
||
pRe->isOpticalDuplicate = true;
|
||
zzhopticalSet.insert(pRe->read1IndexInFile);
|
||
zzhopticalSet.insert(pRe->read2IndexInFile);
|
||
zzhopticalArr.push_back(pRe->read1IndexInFile);
|
||
zzhopticalArr.push_back(pRe->read2IndexInFile);
|
||
} else {
|
||
pRe->isOpticalDuplicate = false;
|
||
zzhopticalSet.erase(pRe->read1IndexInFile);
|
||
zzhopticalSet.erase(pRe->read2IndexInFile);
|
||
}
|
||
}
|
||
return opticalDuplicates;
|
||
}
|
||
|
||
/**
|
||
* 记录光学原因造成的冗余
|
||
*/
|
||
void trackOpticalDuplicates(vector<const ReadEnds *> &readEndsArr, const ReadEnds *pBestRe) {
|
||
bool hasFR = false, hasRF = false;
|
||
int prevOpticalDupNum = 0;
|
||
// Check to see if we have a mixture of FR/RF
|
||
for (auto pRe : readEndsArr) {
|
||
if (pRe->isOpticalDuplicate)
|
||
++prevOpticalDupNum;
|
||
if (ReadEnds::FR == pRe->orientationForOpticalDuplicates)
|
||
hasFR = true;
|
||
else if (ReadEnds::RF == pRe->orientationForOpticalDuplicates)
|
||
hasRF = true;
|
||
}
|
||
|
||
// Check if we need to partition since the orientations could have changed
|
||
int nOpticalDup;
|
||
if (hasFR && hasRF) { // need to track them independently
|
||
vector<const ReadEnds *> trackOpticalDuplicatesF;
|
||
vector<const ReadEnds *> trackOpticalDuplicatesR;
|
||
// Split into two lists: first of pairs and second of pairs,
|
||
// since they must have orientation and same starting end
|
||
for (auto pRe: readEndsArr) {
|
||
if (ReadEnds::FR == pRe->orientationForOpticalDuplicates)
|
||
trackOpticalDuplicatesF.push_back(pRe);
|
||
else if (ReadEnds::RF == pRe->orientationForOpticalDuplicates)
|
||
trackOpticalDuplicatesR.push_back(pRe);
|
||
else
|
||
cerr << "Found an unexpected orientation: " << pRe->orientation << endl;
|
||
}
|
||
// track the duplicates
|
||
int nOpticalDupF = checkOpticalDuplicates(trackOpticalDuplicatesF, pBestRe);
|
||
int nOpticalDupR = checkOpticalDuplicates(trackOpticalDuplicatesR, pBestRe);
|
||
nOpticalDup = nOpticalDupF + nOpticalDupR;
|
||
} else { // No need to partition
|
||
nOpticalDup = checkOpticalDuplicates(readEndsArr, pBestRe);
|
||
}
|
||
|
||
// trackDuplicateCounts
|
||
gMetrics.DuplicateCountHist += readEndsArr.size() - nOpticalDup;
|
||
if (readEndsArr.size() > nOpticalDup)
|
||
gMetrics.NonOpticalDuplicateCountHist += readEndsArr.size() - nOpticalDup;
|
||
if (nOpticalDup)
|
||
gMetrics.OpticalDuplicatesCountHist += nOpticalDup + 1;
|
||
|
||
|
||
gMetrics.OpticalDuplicatesByLibraryId += nOpticalDup - prevOpticalDupNum;
|
||
//gMetrics.OpticalDuplicatesByLibraryId += nOpticalDup;
|
||
|
||
// cout << "zzh optical:" << (++zzhtestnum) << "\t" << readEndsArr.size() << "\t" << nOpticalDup << endl;
|
||
// cerr << (zzhtestnum++) << " " << readEndsArr.size() << ":" << nOpticalDup << endl;
|
||
} |