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/**
* WHAM - high-throughput sequence aligner
* Copyright (C) 2011 WHAM Group, University of Wisconsin
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/* $Id: hash.cpp 152 2012-07-22 10:52:53Z yinan $ */
#include <stdlib.h>
#include <memory.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <math.h>
#include "hash.h"
#include "embedhash.h"
#include "bitread.h"
#include "error.h"
#include "pair.h"
#include "edit_distance.h"
#include "util.h"
#include "rdtsc.h"
#define BITWISE_ALIGNMENT
//#define DEBUG_PRINT_LIST
unsigned long long statEmbedHashLookup = 0;
unsigned long long statEmbedHashLookupEntry = 0;
EmbedHashTable::EmbedHashTable() {
memset(this, 0, sizeof(EmbedHashTable));
}
EmbedHashTable::~EmbedHashTable() {
delete[] buckets;
delete[] overflowPool;
}
/*
* HashTable::init()
* initialize the private variables
*/
void EmbedHashTable::init(CompactSequence * seq, int len, unsigned int nBucket,
int numError, int nPartition) {
sequence = seq;
length = len;
lenSeq = length * BITS_PER_BASE;
nMismatch = numError;
nMaxError = nMismatch;
nMaxGap = 0;
maxQual = MAX_INT;
if (nBucket == 0) {
double nEntry, nSpace;
nEntry = (double) seq->getNum();
nSpace = pow(8.0, length / nPartition * (nPartition - nMismatch));
numBucket = nEntry < nSpace ? (int) nEntry : (int) nSpace;
} else
numBucket = nBucket;
numBucket = nextPrime(numBucket);
numEmpty = numBucket;
/*
* if the sequence size is greater than 2^31, we have to
* use a normal hash table, otherwise, we use a compressed
* hash table to speedup the searches.
*/
if (seq->getNum() < COMPRESS_TABLE_SIZE
)
compressedTable = true;
else
compressedTable = false;
}
/*
* HashTable::preProcessInit()
* Allocate and initialize the hash bucket array and bitmap arrays
* for collision bits and empty bits.
*/
int EmbedHashTable::preProcessInit() {
/* allocate hash buckets. */
buckets = (unsigned int *) malloc((int64) numBucket * sizeof(unsigned int));
if (buckets == NULL
)
return ERR_MEM;
/*
* allocate bitmap arrays to identify empty buckets
* and collision buckets.
*/
emptyBits = (unsigned char *) malloc((int64) numBucket / BITS_PER_BYTE + 1);
if (emptyBits == NULL
)
return ERR_MEM;
collisionBits = (unsigned char *) malloc(
(int64) numBucket / BITS_PER_BYTE + 1);
if (collisionBits == NULL
)
return ERR_MEM;
/* Initialization */
memset(buckets, 0, numBucket * sizeof(unsigned int));
memset(emptyBits, 0, numBucket / BITS_PER_BYTE + 1);
memset(collisionBits, 0, numBucket / BITS_PER_BYTE + 1);
return SUCCESS;
}
/*
* HashTable::preProcessEnd()
* apply the empty bits and collision bits to the hash buckets.
* For empty buckets, the bucket values are set to be HASH_EMPTY.
* For the buckets with collisions, the most significant bits in
* the buckets are set to be 1.
*/
int EmbedHashTable::preProcessEnd() {
uint32 i;
uint32 tmp, sum = 0;
uint32 collision;
const double ln2 = log(2);
if (buckets == NULL)
{
elog(ERROR, "ERROR: unallocated bucket array in hash table.\n");
return ERR_PARA;
}
if (emptyBits == NULL || collisionBits == NULL)
{
elog(ERROR, "ERROR: unallocated bitmap in hash table.\n");
return ERR_PARA;
}
if (numOverflowEntry < 0)
return ERR_PARA;
/* allicate overflow pool and bitmaps */
overflowPool = (unsigned int *) malloc(
(int64) numOverflowEntry * sizeof(unsigned int));
if (overflowPool == NULL
)
return ERR_MEM;
memset(overflowPool, 0, numOverflowEntry * sizeof(unsigned int));
if (!compressedTable) {
overflowBits = (unsigned char *) malloc(
(int64) numOverflowEntry / BITS_PER_BYTE + 1);
if (overflowBits == NULL
)
return ERR_MEM;
memset(overflowBits, 0,
(numOverflowEntry / BITS_PER_BYTE + 1) * sizeof(char));
}
/*
* scan the hash buckets to appy the empty bits and
* collision bits.
*/
for (i = 0; i < numBucket; i++) {
/*
* The current value of the bucket is the number of collision
* entries in each bucket. We accumulate this value to compute
* the position of the last entries in the overflow array for each bucket,
* and store the position into the bucket. For the non-collision
* buckets, the values will be updated to the position of segment
* in the function insert.
*/
tmp = buckets[i];
sum += tmp;
buckets[i] = sum;
if (buckets[i] > 0) {
if (compressedTable) {
HASH_SET_END(overflowPool[buckets[i] - 1]);
} else {
BITMAP_SET(overflowBits[(buckets[i] - 1) / BITS_PER_BYTE],
(buckets[i] - 1) % BITS_PER_BYTE);
}
}
/* update histogram */
/* int h = 0;
if (tmp > 0)
h = (int)ceil(log(tmp)/ln2);
if (h >= nHistogram)
histogram[nHistogram - 1]++;
else
histogram[h]++;
*/
/* set the values for empty buckets */
if (!BITMAP_IS(emptyBits[i / BITS_PER_BYTE], i % BITS_PER_BYTE))
buckets[i] = HASH_EMPTY;
else {
if (compressedTable) {
/* apply the collision bit to the most significant bit of the bucket */
collision =
BITMAP_IS(collisionBits[i / BITS_PER_BYTE], i % BITS_PER_BYTE);
buckets[i] |= HASH_COLLISION_MASK(collision);
}
}
}
/* free the bitmap arrays */
free(emptyBits);
emptyBits = NULL;
if (compressedTable) {
free(collisionBits);
collisionBits = NULL;
}
// setScanThreshold(0.001);
elog(
DEBUG2,
" numBucket| numEmpty| Collision| numEntry| Col Rat| Emp Rat|Avg List|Avg Miss\n");
elog(
DEBUG2,
"%11u %11u %11u %11u %8.2f %8.2f %8.2f %8.2f\n",
numBucket,
numEmpty,
numCollision,
numEntry,
(double) (numCollision) / (numBucket - numEmpty),
(double) (numEmpty) / (numBucket),
(double) (numOverflowEntry) / numCollision,
(double) (numOverflowEntry + numBucket - numEmpty - numCollision)
/ (numBucket - numEmpty));
return SUCCESS;
}
void EmbedHashTable::setScanThreshold(double r) {
int64 sum = 0;
int64 total = numBucket;
int64 top = total - total * r;
// uint32 top = total - total / 1000;
/*
elog(INFO, "Scan threshold: %f\n", r);
elog(INFO, "Hash List Length Histogram:\n");
elog(INFO, "Empty: %d\n", numEmpty);
for (int i = 0; i < nHistogram - 1; i++) {
sum += histogram[i];
if (sum <= top)
maxScan = 0x1 << (i + 1);
elog(INFO, "List length <= %d: %d (%.2f%%)\n", (0x1 << i), histogram[i], histogram[i] * 100.0 / total);
}
sum += histogram[nHistogram - 1];
if (sum <= top)
maxScan = 0x1 << nHistogram;
elog(INFO, "List length for the rest: %d (%.2f%%)\n", histogram[nHistogram - 1], histogram[nHistogram - 1] * 100.0 / total);
elog(INFO, "Choose maximum of scan: %d\n", maxScan);
*/
}
/*
* HashTable::preProcessInsert()
* update the statistics infos for the hash tables. In particular,
* we update the empty bitmap array and collision bitmap array,
* and update the bucket value to be the number of collision entries
* hashed into the bucket.
*/
void EmbedHashTable::preProcessInsert(int64 * key) {
uint32 bucketID;
numEntry++;
/* compute the hash value */
HASH_FUNCTION(key, numBucket, words, bucketID);
if (!BITMAP_IS(emptyBits[bucketID/BITS_PER_BYTE], bucketID % BITS_PER_BYTE)) {
/* set the empty bit*/
BITMAP_SET(emptyBits[bucketID/BITS_PER_BYTE], bucketID % BITS_PER_BYTE);
numEmpty--;
} else {
if (!BITMAP_IS(collisionBits[bucketID/BITS_PER_BYTE], bucketID % BITS_PER_BYTE)) {
/* The two collsision entries will be added into the overflow array */
BITMAP_SET(collisionBits[bucketID/BITS_PER_BYTE],
bucketID % BITS_PER_BYTE);
numCollision++;
numOverflowEntry += 2;
buckets[bucketID] += 2;
} else {
/* The collsision entry will be added into the overflow array */
numOverflowEntry++;
buckets[bucketID]++;
}
}
}
/*
* HashTable::buildInit()
* allocate and initialize the overflow pool.
*/
int EmbedHashTable::buildInit() {
return SUCCESS;
}
/*
* HashTable::insert()
* insert an segment(entry) into the hash table. If the collision
* bit is 0, the position of the segment is directly stored in the
* hash bucket. Otherwise, the position of the segment is stored in
* the end of the overflow list of the bucket.
*/
void EmbedHashTable::insert(int64 * key, unsigned int offset) {
uint32 curOverflowEntry;
uint32 bucketId;
uint32 seqOffset;
bool collision;
uint32 counter = 0;
int64 * seqVector;
int64 tspace[16];
int64 * target = &tspace[8];
bool isBloomFilter;
uint32 * bloomFilter;
uint32 bloomFilterNum;
seqVector = sequence->getSequence();
/* compute the hash value */
HASH_FUNCTION(key, numBucket, words, bucketId);
if (compressedTable)
collision = HASH_IS_COLLISION(buckets[bucketId]);
else
collision =
BITMAP_IS(collisionBits[bucketId / BITS_PER_BYTE], bucketId % BITS_PER_BYTE);
if (!collision) {
/* store the position into the bucket */
if (compressedTable)
buckets[bucketId] = HASH_GET_OFFSET(offset);
else
buckets[bucketId] = offset;
} else {
buckets[bucketId]--;
/* get the overflow list position */
if (compressedTable)
curOverflowEntry = HASH_GET_OFFSET(buckets[bucketId]);
else
curOverflowEntry = buckets[bucketId];
/*
* append the position of the new segment to the end of
* overflow list.
*/
if (compressedTable)
overflowPool[curOverflowEntry] =
HASH_SET_OFFSET(overflowPool[curOverflowEntry], offset);
else
overflowPool[curOverflowEntry] = offset;
}
}
/*
* HashTable::lookup()
* search the segment(key) on the hash table, find the potential
* matched portions in the genome sequence. Call function
* pairAligner::pairAlign to perform pairwise alignment between
* query sequence and the potential matched portions.
*/
unsigned int EmbedHashTable::lookup(int64 * orgkey, int64 * key, int keyOffset,
char * quals, strand s, int rid, HitSet * hits, bool noGap) {
int num;
uint32 bucketId;
uint32 seqOffset, entryOffset, startOffset;
int64 tspace1[16], tspace2[16];
int64 * diff = &tspace1[8], *target = &tspace2[8];
int64 * seqVector;
bool collision;
uint32 sid, soffset;
int ret;
ErrorVector error;
int nScanEntry = 0;
int rett = SUCCESS;
int maxGap = 0;
if (!noGap)
maxGap = nMaxGap;
seqVector = sequence->getSequence();
/* compute the hash value */
HASH_FUNCTION(key, numBucket, words, bucketId);
if (compressedTable)
collision = HASH_IS_COLLISION(buckets[bucketId]);
else
collision =
BITMAP_IS(collisionBits[bucketId / BITS_PER_BYTE], bucketId % BITS_PER_BYTE);
statEmbedHashLookup++;
if (!collision) {
/* get the position of potential matched portion */
if (compressedTable)
seqOffset = HASH_GET_OFFSET(buckets[bucketId]);
else
seqOffset = buckets[bucketId];
if (seqOffset != HASH_EMPTY)
{
statEmbedHashLookupEntry++;
HASH_DEBUG(printf(" %u", seqOffset - keyOffset / BITS_PER_BASE));
#ifdef DEBUG_HASH_PRINT
BitRead::extract(seqVector, target,
seqOffset * BITS_PER_BASE_LL + lenRest,
lenKey);
if (BitRead::compare(target, key))
printf("*");
#endif
/* get the potential matched portion */
BitRead::extract(seqVector, target,
seqOffset * BITS_PER_BASE_LL - maxGap * BITS_PER_BASE - keyOffset,
lenSeq + maxGap * 2 * BITS_PER_BASE);
nScanEntry++;
/**
* perform the pairwise alignment under the constraint
* on the number of errors.
*/
error = PairAligner::pairAlign(orgkey, target, length, nMaxError, maxGap);
if (error.num <= nMaxError) {
seqOffset = seqOffset - maxGap + error.offset
- keyOffset / BITS_PER_BASE;
if (maxGap != 0) {
/**
* if supports indel, re-extract the matched portion
* with proper offset and length
**/
BitRead::extract(seqVector, target, seqOffset * BITS_PER_BASE_LL,
error.len * BITS_PER_BASE);
}
ret = hits->add(orgkey, target, seqOffset, s, &error, error.qual, rid);
if (ret == MSG_HITSETFULL)
{
HASH_DEBUG(printf(" HIT"));
rett = ret;
}
}
}
// else
// stat_empty++;
} else {
// stat_collision++;
/* get the position of the overflow list */
if (compressedTable)
entryOffset = HASH_GET_OFFSET(buckets[bucketId]);
else
entryOffset = buckets[bucketId];
startOffset = entryOffset;
/* scan the overflow list */
while (entryOffset < numOverflowEntry) {
/* get the position of potential matched portion */
if (compressedTable)
seqOffset = HASH_GET_OFFSET(overflowPool[entryOffset]);
else
seqOffset = overflowPool[entryOffset];
if (seqOffset != HASH_EMPTY)
{
statEmbedHashLookupEntry++;
HASH_DEBUG(printf(" %u", seqOffset - keyOffset / BITS_PER_BASE));
#ifdef DEBUG_HASH_PRINT
BitRead::extract(seqVector, target,
seqOffset * BITS_PER_BASE_LL + lenRest,
lenKey);
if (BitRead::compare(target, key))
printf("*");
#endif
/* get the potential matched portion */
BitRead::extract(seqVector, target,
seqOffset * BITS_PER_BASE_LL - maxGap * BITS_PER_BASE - keyOffset,
lenSeq + maxGap * 2 * BITS_PER_BASE);
nScanEntry++;
/**
* perform the pairwise alignment under the constraint
* on the number of errors.
*/
error = PairAligner::pairAlign(orgkey, target, length, nMaxError,
maxGap);
if (error.num <= nMaxError) {
seqOffset = seqOffset - maxGap + error.offset
- keyOffset / BITS_PER_BASE;
if (maxGap != 0) {
/**
* if supports indel, re-extract the matched portion
* with proper offset and length
**/
BitRead::extract(seqVector, target, seqOffset * BITS_PER_BASE_LL,
error.len * BITS_PER_BASE);
}
ret = hits->add(orgkey, target, seqOffset, s, &error, error.qual,
rid);
if (ret == MSG_HITSETFULL)
{
HASH_DEBUG(printf(" HIT"));
rett = ret;
break;
}
}
}
// if (entryOffset > startOffset + HASH_OVERFLOW_LIST_SCAN_BOUND)
// if (entryOffset > startOffset + 64 * 16)
// break;
if (compressedTable) {
if (HASH_IS_END(overflowPool[entryOffset]))
break;
} else {
if (BITMAP_IS(overflowBits[entryOffset / BITS_PER_BYTE], entryOffset % BITS_PER_BYTE))
break;
}
entryOffset++;
}
}
HASH_DEBUG(printf("\n"));
return rett;
}
/*
* HashTable::save()
* This function is used to save the in-memory hash table on
* disk.
*/
int EmbedHashTable::save(FILE * file) {
size_t ret;
ret = fwrite(this, sizeof(EmbedHashTable), 1, file);
if (ret != 1) {
return ERR_FILE;
}
ret = fwrite(buckets, sizeof(uint32), numBucket, file);
if (ret != numBucket) {
return ERR_FILE;
}
ret = fwrite(overflowPool, sizeof(uint32), numOverflowEntry, file);
if (ret != numOverflowEntry) {
return ERR_FILE;
}
if (!compressedTable) {
ret = fwrite(collisionBits, sizeof(unsigned char),
numBucket / BITS_PER_BYTE + 1, file);
if (ret != numBucket / BITS_PER_BYTE + 1) {
return ERR_FILE;
}
ret = fwrite(overflowBits, sizeof(unsigned char),
numOverflowEntry / BITS_PER_BYTE + 1, file);
if (ret != numOverflowEntry / BITS_PER_BYTE + 1) {
return ERR_FILE;
}
}
return SUCCESS;
}
/*
* HashTable::load()
* This function is used to load the on-disk copy of hash table
* into memory.
*/
int EmbedHashTable::load(FILE * file, CompactSequence * seq) {
size_t ret;
ret = fread(this, sizeof(EmbedHashTable), 1, file);
if (ret != 1) {
elog(ERROR, "failed to load hash table head.\n");
return ERR_FILE;
}
sequence = seq;
/* we can use smaller block to reduct the memory consumption */
buckets = (uint32 *) malloc((int64) numBucket * sizeof(uint32));
if (buckets == NULL)
return ERR_MEM;
ret = fread(buckets, sizeof(uint32), numBucket, file);
if (ret != numBucket) {
elog(ERROR, "failed to load buckets.\n");
return ERR_FILE;
}
overflowPool = (uint32 *) malloc((int64) numOverflowEntry * sizeof(uint32));
if (overflowPool == NULL)
return ERR_MEM;
ret = fread(overflowPool, sizeof(uint32), numOverflowEntry, file);
if (ret != numOverflowEntry) {
elog(ERROR, "failed to load overflow array.\n");
return ERR_FILE;
}
if (!compressedTable) {
collisionBits = (unsigned char *) malloc(
(int64) (numBucket / BITS_PER_BYTE + 1) * sizeof(unsigned char));
if (collisionBits == NULL)
return ERR_MEM;
ret = fread(collisionBits, sizeof(unsigned char),
numBucket / BITS_PER_BYTE + 1, file);
if (ret != numBucket / BITS_PER_BYTE + 1) {
elog(ERROR, "failed to load collision bits.\n");
return ERR_FILE;
}
overflowBits = (unsigned char *) malloc(
(int64) (numOverflowEntry / BITS_PER_BYTE + 1) * sizeof(unsigned char));
if (overflowBits == NULL)
return ERR_MEM;
ret = fread(overflowBits, sizeof(unsigned char),
numOverflowEntry / BITS_PER_BYTE + 1, file);
if (ret != numOverflowEntry / BITS_PER_BYTE + 1) {
elog(ERROR, "failed to load overflow bits. %d %d\n", ret,
numOverflowEntry / BITS_PER_BYTE + 1);
return ERR_FILE;
}
}
return SUCCESS;
}
/*
* HashTable::remove
* free the space occupied by the hash index.
*/
int EmbedHashTable::remove() {
if (buckets) {
free(buckets);
buckets = NULL;
}
if (overflowPool) {
free(overflowPool);
overflowPool = NULL;
}
if (emptyBits) {
free(emptyBits);
emptyBits = NULL;
}
if (collisionBits) {
free(collisionBits);
collisionBits = NULL;
}
return SUCCESS;
}
/*
* nextPrime()
* return the least prime number that is greater
* than the input number.
*/
unsigned int EmbedHashTable::nextPrime(unsigned int num) {
unsigned int i, j, x;
num = num / 2 * 2 + 1;
for (i = num; i < num + 1000; i += 2) {
x = (unsigned int) sqrtl(i);
for (j = 3; j < x; j += 2) {
if (i % j == 0)
break;
}
if (j >= x)
return i;
}
return i;
}
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