1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317
|
#ifndef __KMERHASHMAP_H__
#define __KMERHASHMAP_H__
#include <tr1/tuple>
#include <set>
#include <iostream>
#include <vector>
#include <sstream>
#include <memory>
#include <map>
#include <cstring>
#include <cstdio>
#include <cassert>
#include "DNASeq.hpp"
#include "MMAP.hpp"
struct KmerOccurrence {
unsigned int readID, pos;
KmerOccurrence(unsigned int readID, unsigned pos) : readID(readID),pos(pos) {}
KmerOccurrence() {}
};
class KmerHashMap {
static const unsigned int MaxBinSize;
// Maps Kmers to (read_id, kmer_hit_pos) using Kmer_less comparator.
//
// *** Change hashing structure here ***
// If you use a hashing structure that does not store the objects
// in sorted order, then you will need to sort the kmers later
// as noted below.
std::map<Kmer, std::vector<KmerOccurrence>, Kmer_less> Data;
std::vector<KmerOccurrence> dummy;
unsigned int ihash_st, ihash_ed, nhash;
public:
KmerHashMap() : ihash_st(0),ihash_ed(1),nhash(1) {};
KmerHashMap(unsigned int ihash_st, unsigned int ihash_ed, unsigned int nhash) : ihash_st(ihash_st), ihash_ed(ihash_ed), nhash(nhash) {};
// Retrieve all reads that have the given kmer.
std::vector<KmerOccurrence>& operator[](const Kmer& kmer) {
if(dummy.size()>=MaxBinSize) dummy.clear();
// Only accept if KmerHash falls within the right bucket
// (which is determined below)
// and the size of the bin is correct.
// Otherwise, return a dummy vector.
// 'batch' is which batch of blocks the kmer belongs to.
// The hash table is divided into blocks.
// The blocks are grouped into batches and processed together.
unsigned int batch = Kmer_hash()(kmer) % nhash;
if(batch<ihash_st || batch>=ihash_ed) return dummy;
std::vector<KmerOccurrence>& occ = Data[kmer];
if(occ.size()>=MaxBinSize) return dummy;
return occ;
};
void dump_binary(char* prefix, char* suffix) {
// Number of blocks in a batch.
assert(ihash_ed > ihash_st);
const unsigned int nbatch = ihash_ed - ihash_st;
FILE* fout[nbatch];
FILE* findexout[nbatch];
for(unsigned int i=0; i<nbatch; i++) {
std::ostringstream fname;
std::ostringstream findexname;
// prefix is tmpDIR.
// suffix is the starting read number.
fname << prefix << suffix << ".hash";
findexname << prefix << suffix << ".index";
fout[i] = fopen(fname.str().c_str(), "wb");
findexout[i] = fopen(findexname.str().c_str(), "wb");
}
// compute index
std::vector<std::vector<std::tr1::tuple<Kmer, unsigned int> > > index(nbatch);
for(unsigned int i=0; i<nbatch; i++)
index[i].push_back(std::tr1::make_tuple(Kmer("Z"), 0));
for(std::map<Kmer, std::vector<KmerOccurrence>, Kmer_less>::iterator iter=Data.begin(); iter!=Data.end(); iter++) {
// ibatch is which block the kmer is in (misnomer, should be iblock instead)
unsigned int ibatch = Kmer_hash()(iter->first) % nhash;
assert(ibatch>=ihash_st && ibatch<ihash_ed);
// fnum is the offset of the block within its batch.
unsigned int fnum = ibatch - ihash_st;
// (kmer, # reads that have kmer)
index[fnum].push_back(std::tr1::make_tuple(iter->first, iter->second.size()));
}
// Remove the (Kmer("Z"),0) tuple.
for(unsigned int i=0; i<nbatch; i++)
index[i].erase(index[i].begin());
// ***
// NOTE: Might need to sort the kmers here.
// This is only necessary if we don't use a std::map
// because iterating through std::map iterates in sorted order
// ***
// Write out index.
// Format: kmer string, number of reads with kmer
// nbatch is the number of blocks within a single batch.
for(unsigned int i=0; i<nbatch; i++) {
// Writes out:
// num kmers in block, (kmer, num reads with kmer)+
unsigned int nKmer = index[i].size();
fwrite(&nKmer, sizeof(unsigned int), 1, findexout[i]); // number of kmers
for(unsigned int kid=0; kid<nKmer; kid++) { // index of kmer
const char* kmer = std::tr1::get<0>(index[i][kid]).getKmer().c_str();
unsigned int nread = std::tr1::get<1>(index[i][kid]);
fwrite(kmer, sizeof(char), strlen(kmer)+1, findexout[i]);
fwrite(&nread, sizeof(unsigned int), 1, findexout[i]);
}
}
// Write out reads.
// Format: read ID, hit position
for(unsigned int i=0; i<nbatch; i++) {
// Writes out:
// read id, pos within read
unsigned int nKmer = index[i].size();
for(unsigned int kid=0; kid<nKmer; kid++) {
Kmer kmer = std::tr1::get<0>(index[i][kid]);
std::vector<KmerOccurrence>& occur_list = Data[kmer];
for(std::vector<KmerOccurrence>::iterator occ = occur_list.begin(); occ!=occur_list.end(); occ++) {
const unsigned int& readid = occ->readID;
const unsigned int& pos = occ->pos;
fwrite(&readid, sizeof(unsigned int), 1, fout[i]);
fwrite(&pos, sizeof(unsigned int), 1, fout[i]);
}
}
}
for(unsigned int i=0; i<nbatch; i++) {
fclose(fout[i]);
fclose(findexout[i]);
}
}
}; // end KmerHashMap
class HashMMAP {
MMAP hash_mmap;
MMAP index_mmap;
unsigned int nKmer;
unsigned long long fpos; // index pointer
unsigned long long fpos2; // hash pointer
unsigned long long fbegin; // start of hash block
unsigned long long fend; // end of hash block
unsigned long long f2begin; // start of hash block
unsigned long long f2end; // end of hash block
public:
class ConstReadIterator {
MMAP const &hash_mmap;
unsigned long long fpos2;
public:
ConstReadIterator(MMAP const& hash_mmap, unsigned long long fpos2) : hash_mmap(hash_mmap), fpos2(fpos2) {}
inline unsigned int getReadID() const {
return *(unsigned int*)hash_mmap[fpos2];
if(hash_mmap[fpos2] == NULL) {
std::cout << "ConstReadIterator:: getReadID() out of bounds." << std::endl;
}
}
inline unsigned int getPos() const {
if(hash_mmap[fpos2+sizeof(int)] == NULL) {
std::cout << "ConstReadIterator: getPos() out of bounds." << std::endl;
}
return *(unsigned int*)hash_mmap[fpos2+sizeof(unsigned int)];
}
inline ConstReadIterator& operator++() {
fpos2 += 2 * sizeof(unsigned int);
return *this;
}
inline ConstReadIterator& operator++(int) {
operator++();
return *this;
}
inline bool operator==(ConstReadIterator const &a) const {
return fpos2 == a.fpos2;
}
inline bool operator!=(ConstReadIterator const &a) const {
return !(fpos2 == a.fpos2);
}
};
class ConstIterator {
MMAP const &hash_mmap;
MMAP const &index_mmap;
unsigned long long fpos;
unsigned long long fpos2;
public:
ConstIterator(MMAP const& hash_mmap, MMAP const& index_mmap, unsigned long long fpos, unsigned long long fpos2) : hash_mmap(hash_mmap), index_mmap(index_mmap), fpos(fpos), fpos2(fpos2) {}
inline Kmer getKmer() const {
if(index_mmap[fpos] == NULL) {
std::cout << "getKmer() out of bounds." << std::endl;
}
return Kmer((char*)index_mmap[fpos]);
}
inline unsigned int getOccur() const {
if(index_mmap[fpos] == NULL) {
std::cout << "getOccur() out of bounds." << std::endl;
}
return *(unsigned int*)index_mmap[strlen((char*)index_mmap[fpos]) + 1 + fpos];
}
inline ConstReadIterator read_begin() const {
return ConstReadIterator(hash_mmap, fpos2);
}
inline ConstReadIterator read_end() const {
return ConstReadIterator(hash_mmap, fpos2 + 2*getOccur() * sizeof(unsigned int));
}
inline ConstIterator& operator++() {
int offset = strlen((char*)index_mmap[fpos]) + 1;
if(index_mmap[offset + fpos] == NULL) {
std::cout << "operator++() out of bounds." << std::endl;
}
fpos2 += 2 * (*(unsigned int*)index_mmap[offset + fpos]) * sizeof(unsigned int);
fpos += offset + sizeof(unsigned int);
return *this;
}
inline ConstIterator& operator++(int) {
operator++();
return *this;
}
// Equality depends only on where the index pointer (fpos) points to.
inline bool operator==(ConstIterator const& a) const {
return fpos == a.fpos;
}
inline bool operator!=(ConstIterator const& a) const {
return !(fpos == a.fpos);
}
};
HashMMAP(char* fname, char* findex) : hash_mmap(fname), index_mmap(findex), fpos(0), fpos2(0) {
nKmer = *(unsigned int*)index_mmap[0];
fpos = sizeof(unsigned int);
fbegin = sizeof(unsigned int);
fend = index_mmap.size();
f2begin = 0;
f2end = hash_mmap.size();
}
HashMMAP(char* fname, char* findex, unsigned int ihash_st, unsigned int ihash_ed) : hash_mmap(fname), index_mmap(findex), fpos(0), fpos2(0), fbegin(0), fend(0), f2begin(0), f2end(0) {
nKmer = *(unsigned int*)index_mmap[0];
// I assume all kmers are the same length so just get the
// length of first kmer.
unsigned int len_kmer = strlen((char*)index_mmap[sizeof(unsigned int)])+1;
fpos = fbegin = (len_kmer+sizeof(unsigned int)) * ihash_st + sizeof(unsigned int);
fend = (len_kmer+sizeof(unsigned int)) * ihash_ed + sizeof(unsigned int);
assert(fend <= index_mmap.size());
// Set fpos2 to the correct position.
// Start from beginning of the index.
unsigned long long tmpfpos = sizeof(unsigned int);
fpos2 = 0;
while(tmpfpos < fbegin) {
tmpfpos += len_kmer; // Skip the kmer string.
// Read the number of occurrences.
unsigned int noccur = *(unsigned int*)index_mmap[tmpfpos];
fpos2 += noccur * 2 * sizeof(unsigned int);
tmpfpos += sizeof(unsigned int);
}
assert(tmpfpos == fbegin);
// Set f2begin
f2begin = fpos2;
// Find end position.
// *Continue* from tmpfpos, which was set above.
// (Do not change ordering of these while loops.)
f2end = fpos2;
while(tmpfpos < fend) {
tmpfpos += len_kmer; // Skip the kmer string.
// Read the number of occurrences.
unsigned int noccur = *(unsigned int*)index_mmap[tmpfpos];
f2end += noccur * 2 * sizeof(unsigned int);
tmpfpos += sizeof(unsigned int);
}
assert(f2end <= hash_mmap.size());
}
inline ConstIterator begin() const {
return ConstIterator(hash_mmap, index_mmap, fbegin, f2begin);
}
inline ConstIterator end() const {
return ConstIterator(hash_mmap, index_mmap, fend, f2end);
}
};
#endif
|