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PEAlgnmt.cpp
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PEAlgnmt.cpp
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/*
*
* PEAlgnmt.c
* Soap3(gpu)
*
* Copyright (C) 2011, HKU
*
* 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 2
* 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, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
#include "PEAlgnmt.h"
// --------------------------------------------------
// PE_DEBUG #1
// Uncomment the below to turn on logging message for
// PE matching of two occurrences.
//#define PE_DEBUG_PRINT_MATCHING_PROGRESS
// --------------------------------------------------
// --------------------------------------------------
// PE_DEBUG #2
// Uncomment the below to turn on logging message for
// PE Radix Sort of two occ lists.
//#define PE_DEBUG_PRINT_RADIX_PROGRESS
// --------------------------------------------------
// --------------------------------------------------
// PE_DEBUG #3
// Uncomment the below to turn on visual logging for
// PE matching of two occurrences.
//#define PE_DEBUG_PRINT_VISUAL_MATCHING
// --------------------------------------------------
void PERadixSort ( SRAOccurrence * list, unsigned int count,
SRAOccurrence * buffer1, SRAOccurrence * buffer2,
SRAOccurrence * sortedList );
void PEReportPairResult ( PEOutput * peOutput, SRAOccurrence * occ_1, SRAOccurrence * occ_2, unsigned int insertion );
inline int PEIsPairEndMatch ( PEInput * peInput, SRAOccurrence * occ_1, SRAOccurrence * occ_2, unsigned int * insertion );
inline int PEIsPairOutOfRange ( PEInput * peInput, SRAOccurrence * occ_1, SRAOccurrence * occ_2 );
void PEPairListInitialise ( PEPairList * pePairList );
void PEOutputInitialise ( PEOutput * peOutput );
PEPairList * PEPairListConstruct ();
void PEPairListFree ( PEPairList * pePairList );
/////////////////////////////////////////////////////
/*
Function SRAEnrichSARanges
*/
/////////////////////////////////////////////////////
/*
unsigned int SRAEnrichSARanges(BWT * bwt, HSP * hsp,
unsigned int saIndexLeft, unsigned int saIndexRight,
char * strand, int * mismatchCount) {
}
*/
/////////////////////////////////////////////////////
/*
Function PERetrievePositionFromSAIndex
This function is a place-holder for possibly extension of
PE to use High-Occ data-structure. However unlikely.
*/
/////////////////////////////////////////////////////
inline unsigned int PERetrievePositionFromSAIndex ( BWT * bwt, unsigned int saIndex )
{
unsigned int ambPosition = ( *bwt->_bwtSaValue ) ( bwt, saIndex );
return ambPosition;
}
/////////////////////////////////////////////////////
/*
Function PERetrieveChromoPositioning
*/
/////////////////////////////////////////////////////
void PERetrieveChromoPositioning ( BWT * bwt,
HSP * hsp,
unsigned int ambPosition,
int * sequenceId, unsigned int * offset )
{
unsigned int * ambiguityMap = hsp->ambiguityMap;
Translate * translate = hsp->translate;
unsigned int approxIndex = ambPosition >> GRID_SAMPLING_FACTOR_2_POWER;
unsigned int approxValue = ambiguityMap[approxIndex];
while ( translate[approxValue].startPos > ambPosition )
{
approxValue--;
}
ambPosition -= translate[approxValue].correction;
( *sequenceId ) = translate[approxValue].chrID;
( *offset ) = ambPosition;
}
/////////////////////////////////////////////////////
/*
Function PERadixSort
*/
/////////////////////////////////////////////////////
void PERadixSort ( SRAOccurrence * list, unsigned int count,
SRAOccurrence * buffer1, SRAOccurrence * buffer2,
SRAOccurrence * sortedList )
{
//How many bits we sort each pass
#define PE_RADIX_BIT_PER_PASS 4
//How many pass in total we run the sorting
#define PE_RADIX_PASS 8
//The multiplying result of the two parameters above should be
//greater than the bit-length of the maximum index on the ref.seq.
//e.g. 4 and 8 such that the sorting will cover 32-bit
// which can represent all index in the ref. seq.
unsigned int i, j;
unsigned int base;
int idxIndexSize = ( 1 << PE_RADIX_BIT_PER_PASS );
int radixMask = idxIndexSize - 1;
unsigned int idxRadix[idxIndexSize + 1];
SRAOccurrence * swap;
SRAOccurrence * activeBuffer = buffer1;
SRAOccurrence * oldBuffer = list;
#ifdef PE_DEBUG_PRINT_RADIX_PROGRESS
printf ( " idxIndexSize = %d\n", idxIndexSize );
printf ( " radixMask = %d\n", radixMask );
printf ( " PE_RADIX_BIT_PER_PASS = %d\n", PE_RADIX_BIT_PER_PASS );
printf ( " PE_RADIX_PASS = %d\n", PE_RADIX_PASS );
#endif
for ( base = 0; base < PE_RADIX_PASS; base++ )
{
//Initialise idxRadix
for ( i = 0; i <= idxIndexSize; i++ )
{
idxRadix[i] = 0;
}
//Count oldBuffer into activeBuffer
for ( i = 0; i < count; i++ )
{
unsigned int key = oldBuffer[i].ambPosition;
key = key >> base * PE_RADIX_BIT_PER_PASS;
key &= radixMask;
idxRadix[key + 1]++;
}
//Post-process idxRadix
for ( i = 1; i <= idxIndexSize; i++ )
{
idxRadix[i] += idxRadix[i - 1];
}
//Move oldBuffer into activeBuffer with ordering
for ( i = 0; i < count; i++ )
{
unsigned int key = oldBuffer[i].ambPosition;
key = key >> base * PE_RADIX_BIT_PER_PASS;
key &= radixMask;
activeBuffer[idxRadix[key]].ambPosition = oldBuffer[i].ambPosition;
activeBuffer[idxRadix[key]].mismatchCount = oldBuffer[i].mismatchCount;
activeBuffer[idxRadix[key]].strand = oldBuffer[i].strand;
idxRadix[key]++;
}
//Swap double buffer
swap = activeBuffer;
if ( base == 0 )
{
activeBuffer = buffer2;
}
else
{
activeBuffer = oldBuffer;
}
oldBuffer = swap;
}
//Count oldBuffer into sortedlist
for ( i = 0; i < count; i++ )
{
sortedList[i].ambPosition = oldBuffer[i].ambPosition;
sortedList[i].mismatchCount = oldBuffer[i].mismatchCount;
sortedList[i].strand = oldBuffer[i].strand;
}
}
inline void PEMappingCore ( PEInput * peInput, PEOutput * peOutput,
SRAOccurrence * occList_1, unsigned int occCount_1,
SRAOccurrence * occList_2, unsigned int occCount_2 )
{
// ATTENTION : BRUTE FORCE ENGINE
//---------------------------------------------------------
/*unsigned int occIndex_First = 0;
unsigned int occIndex_Last = 0;
for (occIndex_1=0;occIndex_1<occCount_1;occIndex_1++) {
int flag = 0;
for (occIndex_2=occIndex_First;occIndex_2<occCount_2;occIndex_2++) {
if (PEIsPairEndMatch(peInput, &(occList_1[occIndex_1]), &(occList_2[occIndex_2]))) {
if (flag==0) {
occIndex_First = occIndex_2;
flag=1;
}
//Output answer
PEReportPairResult(peOutput,&(occList_1[occIndex_1]),&(occList_2[occIndex_2]));
occIndex_Last = occIndex_2;
}
if (PEIsPairOutOfRange(peInput, &(occList_1[occIndex_1]), &(occList_2[occIndex_2]))) {
break;
}
}
}*/
// ATTENTION : BRUTE FORCE ENGINE - MARK 2
//---------------------------------------------------------
unsigned long i;
unsigned long occIndex_1 = 0;
unsigned long occIndex_2 = 0;
int OutputType = peInput->OutputType;
int strandLeftLeg = peInput->strandLeftLeg;
int strandRightLeg = peInput->strandRightLeg;
unsigned int insertion;
while ( occIndex_1 < occCount_1 && occIndex_2 < occCount_2 )
{
if ( occList_1[occIndex_1].ambPosition <= occList_2[occIndex_2].ambPosition )
{
if ( occList_1[occIndex_1].strand == strandLeftLeg )
{
for ( i = occIndex_2; i < occCount_2; i++ )
{
if ( PEIsPairEndMatch ( peInput, & ( occList_1[occIndex_1] ), & ( occList_2[i] ), &insertion ) )
{
PEReportPairResult ( peOutput, & ( occList_1[occIndex_1] ), & ( occList_2[i] ), insertion );
if ( OutputType == PE_REPORT_ONE ) { break; }
}
if ( PEIsPairOutOfRange ( peInput, & ( occList_1[occIndex_1] ), & ( occList_2[i] ) ) )
{
break;
}
}
}
occIndex_1++;
}
else
{
#ifndef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
if ( occList_2[occIndex_2].strand == strandLeftLeg )
{
for ( i = occIndex_1; i < occCount_1; i++ )
{
if ( PEIsPairEndMatch ( peInput, & ( occList_2[occIndex_2] ), & ( occList_1[i] ), &insertion ) )
{
PEReportPairResult ( peOutput, & ( occList_1[i] ), & ( occList_2[occIndex_2] ), insertion );
if ( OutputType == PE_REPORT_ONE ) { break; }
}
if ( PEIsPairOutOfRange ( peInput, & ( occList_2[occIndex_2] ), & ( occList_1[i] ) ) )
{
break;
}
}
}
#endif
occIndex_2++;
}
}
//---------------------------------------------------------
}
/////////////////////////////////////////////////////
/*
Function PEValidateAndPreparePEInput
*/
/////////////////////////////////////////////////////
inline int PEValidateAndPreparePEInput ( PEInput * peInput )
{
int isValid = 1;
int isWarning = 0;
if ( peInput->bwt == NULL || peInput->hsp == NULL )
{
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "[PEValidateAndPreparePEInput] BWT/HSP index missing.\n" );
#endif
isValid = 0;
}
if ( peInput->OutputType != PE_REPORT_ALL &&
peInput->OutputType != PE_REPORT_ONE )
{
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "[PEValidateAndPreparePEInput] Defaulting Output Type.\n" );
#endif
peInput->OutputType = PE_REPORT_ALL;
isWarning = 1;
}
if ( peInput->strandLeftLeg == PE_NON_INPUT_VALUE ||
peInput->strandRightLeg == PE_NON_INPUT_VALUE )
{
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "[PEValidateAndPreparePEInput] Defaulting strandLeftLeg / strandRightLeg.\n" );
#endif
peInput->strandLeftLeg = QUERY_POS_STRAND;
peInput->strandRightLeg = QUERY_NEG_STRAND;
isWarning = 1;
}
if ( peInput->patternLength == PE_NON_INPUT_VALUE )
{
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "[PEValidateAndPreparePEInput] patternLength missing.\n" );
#endif
isValid = 0;
}
if ( ( peInput->insertSizeMean == PE_NON_INPUT_VALUE ||
peInput->insertSizeStdDev == PE_NON_INPUT_VALUE ) &&
( peInput->insertLbound == PE_NON_INPUT_VALUE ||
peInput->insertUbound == PE_NON_INPUT_VALUE ) )
{
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "[PEValidateAndPreparePEInput] insertion size parameter missing.\n" );
#endif
isValid = 0;
}
if ( peInput->insertLbound == PE_NON_INPUT_VALUE ||
peInput->insertUbound == PE_NON_INPUT_VALUE )
{
peInput->insertLbound = peInput->insertSizeMean - 3 * peInput->insertSizeStdDev;
peInput->insertUbound = peInput->insertSizeMean + 3 * peInput->insertSizeStdDev;
}
return isValid;
}
/////////////////////////////////////////////////////
/*
Function PEMapping
*/
/////////////////////////////////////////////////////
void PEMapping ( PEInput * peInput, PEOutput * peOutput,
PESRAAlignmentResult * resultListA, unsigned int resultCountA,
PESRAAlignmentResult * resultListB, unsigned int resultCountB )
{
//2BWT Index parameter
BWT * bwt = peInput->bwt;
HSP * hsp = peInput->hsp;
//Declare variables
unsigned int i, j;
int k;
unsigned int allocMemory = 0;
//These sort buffer will be used as double buffer for the sorting
SRAOccurrence * sortBuffer_1;
SRAOccurrence * sortBuffer_2;
SRAOccurrence * occList_1;
SRAOccurrence * occList_2;
unsigned int occIndex_1, occIndex_2;
//Initialise the peOutput
PEOutputInitialise ( peOutput );
//enrich the peInput
// [m - 3 * sd, m + 3 * sd], and the
if ( !PEValidateAndPreparePEInput ( peInput ) )
{
peOutput->flag = PE_ALIGNMENT_INPUT_ERROR;
return;
}
//More information about the occurrence list
unsigned int occCount_1 = 0, occCount_2 = 0;
unsigned int occMaxCount = 0;
for ( i = 0; i < resultCountA; i++ )
{
occCount_1 += resultListA[i].saIndexRight - resultListA[i].saIndexLeft + 1;
}
for ( i = 0; i < resultCountB; i++ )
{
occCount_2 += resultListB[i].saIndexRight - resultListB[i].saIndexLeft + 1;
}
occMaxCount = occCount_1;
if ( occMaxCount < occCount_2 )
{
occMaxCount = occCount_2;
}
//Allocate enough memory for all occurrences
//We need at most (4 x max(occCount_1,occCount_2) x 10 Bytes (SRAOccurrence) in total for PE mapping.
//Assuming we have at least 256-Megabyte left in main memory
#define PE_ALLOCATED_BYTE 268435456
allocMemory = 4 * occMaxCount * sizeof ( SRAOccurrence );
if ( allocMemory > PE_ALLOCATED_BYTE )
{
fprintf ( stderr, "Insufficient memory to proceed. %u required exceeded %u.\n", allocMemory, PE_ALLOCATED_BYTE );
exit ( 1 );
}
sortBuffer_1 = ( SRAOccurrence * ) malloc ( occMaxCount * sizeof ( SRAOccurrence ) ) ;
sortBuffer_2 = ( SRAOccurrence * ) malloc ( occMaxCount * sizeof ( SRAOccurrence ) ) ;
occList_1 = ( SRAOccurrence * ) malloc ( occCount_1 * sizeof ( SRAOccurrence ) ) ;
occList_2 = ( SRAOccurrence * ) malloc ( occCount_2 * sizeof ( SRAOccurrence ) ) ;
//Retrieve the occurrences
occIndex_1 = 0;
for ( i = 0; i < resultCountA; i++ )
{
for ( j = resultListA[i].saIndexLeft; j <= resultListA[i].saIndexRight; j++ )
{
occList_1[occIndex_1].ambPosition = PERetrievePositionFromSAIndex ( bwt, j );
occList_1[occIndex_1].strand = resultListA[i].strand;
occList_1[occIndex_1].mismatchCount = resultListA[i].mismatchCount;
occIndex_1++;
}
}
occIndex_2 = 0;
for ( i = 0; i < resultCountB; i++ )
{
for ( j = resultListB[i].saIndexLeft; j <= resultListB[i].saIndexRight; j++ )
{
occList_2[occIndex_2].ambPosition = PERetrievePositionFromSAIndex ( bwt, j );
occList_2[occIndex_2].strand = resultListB[i].strand;
occList_2[occIndex_2].mismatchCount = resultListB[i].mismatchCount;
occIndex_2++;
}
}
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "%u(%u) positions are retrieved from %u SA ranges.\n", occIndex_1, occCount_1, resultCountA );
printf ( "%u(%u) positions are retrieved from %u SA ranges.\n", occIndex_2, occCount_2, resultCountB );
#endif
//Radix sort the lists
PERadixSort ( occList_1, occCount_1, sortBuffer_1, sortBuffer_2, occList_1 );
PERadixSort ( occList_2, occCount_2, sortBuffer_1, sortBuffer_2, occList_2 );
//Calling the core
PEMappingCore ( peInput, peOutput, occList_1, occCount_1, occList_2, occCount_2 );
peOutput->flag = PE_ALIGNMENT_COMPLETED;
free ( sortBuffer_1 );
free ( sortBuffer_2 );
free ( occList_1 );
free ( occList_2 );
}
/////////////////////////////////////////////////////
/*
Function PEMappingOccurrences
*/
/////////////////////////////////////////////////////
void PEMappingOccurrences ( PEInput * peInput, PEOutput * peOutput,
SRAOccurrence * occList_1, unsigned int occCount_1,
SRAOccurrence * occList_2, unsigned int occCount_2 )
{
//2BWT Index parameter
BWT * bwt = peInput->bwt;
HSP * hsp = peInput->hsp;
//Declare variables
unsigned int i, j;
int k;
unsigned int allocMemory = 0;
//These sort buffer will be used as double buffer for the sorting
SRAOccurrence * sortBuffer_1;
SRAOccurrence * sortBuffer_2;
unsigned int occIndex_1, occIndex_2;
//Initialise the peOutput
PEOutputInitialise ( peOutput );
//enrich the peInput
// [m - 3 * sd, m + 3 * sd], and the
if ( !PEValidateAndPreparePEInput ( peInput ) )
{
peOutput->flag = PE_ALIGNMENT_INPUT_ERROR;
return;
}
//More information about the occurrence list
unsigned int occMaxCount = 0;
occMaxCount = occCount_1;
if ( occMaxCount < occCount_2 )
{
occMaxCount = occCount_2;
}
//Allocate enough memory for all occurrences
//We need at most (4 x max(occCount_1,occCount_2) x 10 Bytes (SRAOccurrence) in total for PE mapping.
//Assuming we have at least 256-Megabyte left in main memory
#define PE_ALLOCATED_BYTE 268435456
allocMemory = 4 * occMaxCount * sizeof ( SRAOccurrence );
if ( allocMemory > PE_ALLOCATED_BYTE )
{
fprintf ( stderr, "Insufficient memory to proceed. %u required exceeded %u.\n", allocMemory, PE_ALLOCATED_BYTE );
exit ( 1 );
}
sortBuffer_1 = ( SRAOccurrence * ) malloc ( occMaxCount * sizeof ( SRAOccurrence ) ) ;
sortBuffer_2 = ( SRAOccurrence * ) malloc ( occMaxCount * sizeof ( SRAOccurrence ) ) ;
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "%u positions in list 1.\n", occCount_1 );
printf ( "%u positions in list 2.\n", occCount_2 );
#endif
//Radix sort the lists
if ( occCount_1 > 1 )
{ PERadixSort ( occList_1, occCount_1, sortBuffer_1, sortBuffer_2, occList_1 ); }
if ( occCount_2 > 1 )
{ PERadixSort ( occList_2, occCount_2, sortBuffer_1, sortBuffer_2, occList_2 ); }
//Calling the core
PEMappingCore ( peInput, peOutput, occList_1, occCount_1, occList_2, occCount_2 );
peOutput->flag = PE_ALIGNMENT_COMPLETED;
free ( sortBuffer_1 );
free ( sortBuffer_2 );
}
/////////////////////////////////////////////////////
/*
Function PEIsPairEndMatch
This function takes in 2 occurrence and determind
if the two occurrences form a pair end mapping.
Assume occ_1 <= occ_2.
Input:
peInput - The input parameter for PE
occ_1 - The occurrence on left leg
occ_2 - The occurrence on right leg
Output:
1 if the two occurrences form a pair end mapping
0 otherwise
*/
/////////////////////////////////////////////////////
inline int PEIsPairEndMatch ( PEInput * peInput, SRAOccurrence * occ_1, SRAOccurrence * occ_2, unsigned int * insertion )
{
//For a valid paired-end reads,
// let the mean and the standard deviation of the insert size be "m" and "sd",
// the distance between the leftmost of the left-read alignment and the rightmost
// of the right-read alignment should fall between [m - 3 * sd, m + 3 * sd], and the
// strand of the left-read alignment is NOT the same as the strand of the right-read alignment.
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( "PEIsPairEndMatch is invoked.\n" );
printf ( " pos = %u \t strand = %d \n", occ_1->ambPosition, occ_1->strand );
printf ( " pos = %u \t strand = %d \n", occ_2->ambPosition, occ_2->strand );
#endif
int strandLeftLeg = peInput->strandLeftLeg;
int strandRightLeg = peInput->strandRightLeg;
int strandCheck = ( occ_1->strand == strandLeftLeg &&
occ_2->strand == strandRightLeg );
//positions are left aligned, therefore it requires correction
unsigned int ambPos_2 = occ_2->ambPosition + peInput->patternLength - 1;
//occ_2->ambPosition += peInput->patternLength - 1;
unsigned int gap = ambPos_2 - occ_1->ambPosition + 1;
( *insertion ) = gap;
#ifdef PE_DEBUG_PRINT_VISUAL_MATCHING
char DEBUG_sorted[2];
DEBUG_sorted[0] = 'X';
DEBUG_sorted[1] = ' ';
printf ( " %10llu <----- %10llu -----> %10llu [%d:%d] %c\n", occ_1->ambPosition, gap, ambPos_2, peInput->insertLbound, peInput->insertUbound, DEBUG_sorted[ ( occ_1->ambPosition <= ambPos_2 ) & 1] );
#endif
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( " lbound = %u \t gap = %u \t ubound = %u\n", peInput->insertLbound, gap, peInput->insertUbound );
#endif
return ( ( peInput->insertLbound <= gap ) && ( gap <= peInput->insertUbound ) && strandCheck );
}
inline int PEIsPairOutOfRange ( PEInput * peInput, SRAOccurrence * occ_1, SRAOccurrence * occ_2 )
{
if ( occ_1->strand == occ_2->strand ) { return 0; }
unsigned int occ_1_pos = occ_1->ambPosition + peInput->insertUbound;
unsigned int occ_2_pos = occ_2->ambPosition + peInput->patternLength - 1;
return occ_1_pos < occ_2_pos;
}
void PEReportPairResult ( PEOutput * peOutput, SRAOccurrence * occ_1, SRAOccurrence * occ_2, unsigned int insertion )
{
#ifdef PE_DEBUG_PRINT_MATCHING_PROGRESS
printf ( " Pair-end alignment is found.\n" );
#endif
PEPairList * pePairList = peOutput->tail;
if ( pePairList->pairsCount == PE_MAX_BUCKET_SIZE )
{
if ( pePairList->next == NULL )
{
pePairList->next = PEPairListConstruct ();
}
pePairList = pePairList->next;
peOutput->tail = pePairList;
}
PEPairs * pePair = & ( pePairList->pairs[pePairList->pairsCount] );
pePair->algnmt_1 = occ_1->ambPosition;
pePair->strand_1 = occ_1->strand;
pePair->mismatch_1 = occ_1->mismatchCount;
pePair->algnmt_2 = occ_2->ambPosition;
pePair->strand_2 = occ_2->strand;
pePair->mismatch_2 = occ_2->mismatchCount;
pePair->insertion = insertion;
pePair->totalMismatchCount = occ_1->mismatchCount + occ_2->mismatchCount;
pePairList->pairsCount++;
}
/*
unsigned int PEMappingToDisk(PEInput * peInput, PEPairList * pePairList) {
}
*/
/////////////////////////////////////////////////////
// Constructor and Destructor
/////////////////////////////////////////////////////
PEInput * PEInputConstruct ( BWT * bwt, HSP * hsp )
{
PEInput * peInput = ( PEInput * ) malloc ( sizeof ( PEInput ) );
peInput->bwt = bwt;
peInput->hsp = hsp;
peInput->patternLength = PE_NON_INPUT_VALUE;
peInput->strandLeftLeg = PE_NON_INPUT_VALUE;
peInput->strandRightLeg = PE_NON_INPUT_VALUE;
peInput->insertSizeMean = PE_NON_INPUT_VALUE;
peInput->insertSizeStdDev = PE_NON_INPUT_VALUE;
peInput->insertLbound = PE_NON_INPUT_VALUE;
peInput->insertUbound = PE_NON_INPUT_VALUE;
peInput->OutputType = PE_REPORT_ALL;
return peInput;
}
void PEInputFree ( PEInput * peInput )
{
free ( peInput );
}
void PEPairListInitialise ( PEPairList * pePairList )
{
if ( pePairList == NULL ) { return; }
PEPairListInitialise ( pePairList->next );
pePairList->pairsCount = 0;
}
void PEOutputInitialise ( PEOutput * peOutput )
{
PEPairListInitialise ( peOutput->root );
peOutput->tail = peOutput->root;
peOutput->flag = PE_ALIGNMENT_INITIALISED;
}
PEPairList * PEPairListConstruct ()
{
PEPairList * pePairList = ( PEPairList * ) malloc ( sizeof ( PEPairList ) );
pePairList->pairsCount = 0;
pePairList->next = NULL;
return pePairList;
}
PEOutput * PEOutputConstruct ()
{
PEOutput * peOutput = ( PEOutput * ) malloc ( sizeof ( PEOutput ) );
peOutput->root = PEPairListConstruct ();
peOutput->tail = peOutput->root;
return peOutput;
}
void PEPairListFree ( PEPairList * pePairList )
{
if ( pePairList == NULL ) { return; }
PEPairListFree ( pePairList->next );
free ( pePairList );
}
void PEOutputFree ( PEOutput * peOutput )
{
PEPairListFree ( peOutput->root );
free ( peOutput );
}
/////////////////////////////////////////////////////
// Utilities
/////////////////////////////////////////////////////
void PEPrintOccurrenceList ( const char * listName, SRAOccurrence * list, unsigned int length )
{
unsigned int i;
printf ( "List of occurrences %s =\n", listName );
for ( i = 0; i < length; i++ )
{
printf ( "%u ", list[i].ambPosition );
if ( ( i + 1 ) % 8 == 0 ) {printf ( "\n" );}
}
printf ( "\n" );
}
void PEPrintPEPairList ( PEPairList * pairList, int maxOutput )
{
int i;
int j = 0;
char strand[3];
strand[1] = '+';
strand[2] = '-';
while ( pairList != NULL && pairList->pairsCount > 0 )
{
for ( i = 0; i < pairList->pairsCount; i++ )
{
PEPairs * pePair = & ( pairList->pairs[i] );
printf ( "algnmt_1 = %u(%c) algnmt_2 = %u(%c)\n",
pePair->algnmt_1, strand[pePair->strand_1],
pePair->algnmt_2, strand[pePair->strand_2] );
j++;
if ( j >= maxOutput && maxOutput >= 0 ) { return; }
}
pairList = pairList->next;
}
}
void PEPrintPEOutput ( PEOutput * peOutput )
{
PEPrintPEPairList ( peOutput->root, -1 );
}
void PEPrintPEOutputWithLimit ( PEOutput * peOutput, int maxOutput )
{
PEPrintPEPairList ( peOutput->root, maxOutput );
}
unsigned int PECountPEPairList ( PEPairList * pairList )
{
unsigned int count = 0;
while ( pairList != NULL && pairList->pairsCount > 0 )
{
count += pairList->pairsCount;
pairList = pairList->next;
}
return count;
}
unsigned int PECountPEOutput ( PEOutput * peOutput )
{
return PECountPEPairList ( peOutput->root );
}
unsigned int PEStatsPEPairList ( PEPairList * pairList, PEPairs ** optimal, PEPairs ** suboptimal, unsigned int * mismatchStats )
{
unsigned int count = 0;
unsigned int i;
PEPairs * iOptimal = NULL;
PEPairs * iSubOptimal = NULL;
uint8_t iOptimal_MismatchCount = 255;
uint8_t iOptimal_MismatchDiff = 255;
uint8_t iSubOptimal_MismatchCount = 255;
uint8_t iSubOptimal_MismatchDiff = 255;
while ( pairList != NULL && pairList->pairsCount > 0 )
{
count += pairList->pairsCount;
for ( i = 0; i < pairList->pairsCount; i++ )
{
PEPairs * pePair = & ( pairList->pairs[i] );
int numMismatchOnPE = pePair->totalMismatchCount;
mismatchStats[numMismatchOnPE]++;
int diffMismatch = pePair->mismatch_1 - pePair->mismatch_2;
if ( pePair->mismatch_2 > pePair->mismatch_1 )
{
diffMismatch = -diffMismatch;
}
if ( numMismatchOnPE < iOptimal_MismatchCount )
{
iSubOptimal_MismatchCount = iOptimal_MismatchCount;
iSubOptimal_MismatchDiff = iOptimal_MismatchDiff;
iSubOptimal = iOptimal;
iOptimal = pePair;
iOptimal_MismatchCount = numMismatchOnPE;
iOptimal_MismatchDiff = diffMismatch;
}
else if ( numMismatchOnPE == iOptimal_MismatchCount &&
diffMismatch < iOptimal_MismatchDiff )
{
iOptimal = pePair;
iOptimal_MismatchCount = numMismatchOnPE;
iOptimal_MismatchDiff = diffMismatch;
}
}
pairList = pairList->next;
}
( *optimal ) = iOptimal;
( *suboptimal ) = iSubOptimal;
return count;
}
unsigned int PEStatsPEOutput ( PEOutput * peOutput, PEPairs ** optimal, PEPairs ** suboptimal, unsigned int * mismatchStats )
{
return PEStatsPEPairList ( peOutput->root, optimal, suboptimal, mismatchStats );
}
// Construct the structure ReadInputForDP for each CPU thread
ReadInputForDP * constructReadInputForDP ( int cpuNum )
{
ReadInputForDP * readInput;
readInput = ( ReadInputForDP * ) malloc ( sizeof ( ReadInputForDP ) );
readInput->readNum = 0;
unsigned int initial_size_sa_list = INITIAL_SIZE_SA_LIST_FOR_DP / cpuNum;
unsigned int initial_size_occ_list = INITIAL_SIZE_OCC_LIST_FOR_DP / cpuNum;
readInput->sa_list = ( PESRAAlignmentResult * ) malloc ( initial_size_sa_list * sizeof ( PESRAAlignmentResult ) );
readInput->occ_list = ( SRAOccurrence * ) malloc ( initial_size_occ_list * sizeof ( SRAOccurrence ) );
readInput->saRangeTotalNum = 0;
readInput->occTotalNum = 0;
readInput->saListSize = initial_size_sa_list;
readInput->occListSize = initial_size_occ_list;
readInput->lastReadID = 0xFFFFFFFF;
return readInput;
}
// Reset the structure ReadInputForDP
void resetReadInputForDP ( ReadInputForDP * readInput )
{
readInput->readNum = 0;
readInput->saRangeTotalNum = 0;
readInput->occTotalNum = 0;
}
// Release the memory for the structure ReadInputForDP
void freeReadInputForDP ( ReadInputForDP * readInput )
{
free ( readInput->sa_list );
free ( readInput->occ_list );
free ( readInput );
}
// To add the alignment results of a read to ReadInputForDP
void addToReadInputForDP ( ReadInputForDP * readInput, unsigned int readid, PESRAAlignmentResult * saList, unsigned int saNum,
SRAOccurrence * occList, unsigned int occNum )
{
if ( saNum > 0 )
{
if ( readInput->saRangeTotalNum + saNum > readInput->saListSize )
{
// enlarge the arrays "sa_list" by at least double
unsigned int new_size = readInput->saListSize * 2;
while ( readInput->saRangeTotalNum + saNum > new_size )
{
new_size *= 2;
}
PESRAAlignmentResult * new_sa_list = ( PESRAAlignmentResult * ) malloc ( sizeof ( PESRAAlignmentResult ) * new_size );
memcpy ( new_sa_list, readInput->sa_list, sizeof ( PESRAAlignmentResult ) *readInput->saRangeTotalNum );
free ( readInput->sa_list );
readInput->sa_list = new_sa_list;
readInput->saListSize = new_size;
}
// PESRAAlignmentResult* saListPtr = readInput->sa_list+readInput->saRangeTotalNum;
// memcpy(saListPtr,saList,sizeof(PESRAAlignmentResult)*saNum);
for ( unsigned int i = 0; i < saNum; i++ )
{
readInput->sa_list[i + readInput->saRangeTotalNum] = saList[i];
readInput->sa_list[i + readInput->saRangeTotalNum].readID = readid;
}
readInput->saRangeTotalNum += saNum;
}
if ( occNum > 0 )
{
if ( readInput->occTotalNum + occNum > readInput->occListSize )
{
// enlarge the arrays "occ_list" by at least double
unsigned int new_size = readInput->occListSize * 2;
while ( readInput->occTotalNum + occNum > new_size )
{
new_size *= 2;
}
SRAOccurrence * new_occ_list = ( SRAOccurrence * ) malloc ( sizeof ( SRAOccurrence ) * new_size );
memcpy ( new_occ_list, readInput->occ_list, sizeof ( SRAOccurrence ) *readInput->occTotalNum );
free ( readInput->occ_list );
readInput->occ_list = new_occ_list;
readInput->occListSize = new_size;
}
// SRAOccurrence* occListPtr = readInput->occ_list+readInput->occTotalNum;
// memcpy(occListPtr,occList,sizeof(SRAOccurrence)*occNum);
for ( unsigned int i = 0; i < occNum; i++ )
{
readInput->occ_list[i + readInput->occTotalNum] = occList[i];
readInput->occ_list[i + readInput->occTotalNum].readID = readid;
}
readInput->occTotalNum += occNum;
}
// if (saNum > 0 || occNum > 0)
unsigned int evenid = readid / 2 * 2;
if ( evenid != readInput->lastReadID )
{
readInput->readNum++;
readInput->lastReadID = evenid;
}
}
DynamicUint8Array * DynamicUint8ArrayConstruct ()
{
DynamicUint8Array * newuint8Array = ( DynamicUint8Array * ) malloc ( sizeof ( DynamicUint8Array ) );
newuint8Array->charStr = ( uint8_t * ) malloc ( sizeof ( uint8_t ) * INITIAL_SIZE_CHAR_ARRAY );
newuint8Array->charStr[0] = '\0';
newuint8Array->size = INITIAL_SIZE_CHAR_ARRAY;
newuint8Array->length = 0;
return newuint8Array;
}
void DynamicUint8ArrayFree ( DynamicUint8Array * uint8Array )
{
free ( uint8Array->charStr );
free ( uint8Array );
}
void DynamicUint8ArrayReset ( DynamicUint8Array * uint8Array )
{
uint8Array->length = 0;
uint8Array->charStr[0] = '\0';
}
void appendStringToUint8Array ( DynamicUint8Array * uint8Array, char * charString, int len )
{
while ( uint8Array->length + len >= uint8Array->size )
{
// double the size
uint8_t * newArray = ( uint8_t * ) malloc ( sizeof ( uint8_t ) * uint8Array->size * 2 );
memcpy ( newArray, uint8Array->charStr, uint8Array->length );
free ( uint8Array->charStr );
uint8Array->charStr = newArray;
uint8Array->size = uint8Array->size * 2;
}
memcpy ( uint8Array->charStr + uint8Array->length, charString, len );
uint8Array->length += len;
uint8Array->charStr[uint8Array->length] = '\0';
}
// ================================================
// To hold a set of single-end alignment results
// ================================================
AllHits * constructAllHits ()
{
AllHits * newAllHits = ( AllHits * ) malloc ( sizeof ( AllHits ) );
newAllHits->hitArray = ( Algnmt * ) malloc ( sizeof ( Algnmt ) * SIZE_1_M );
newAllHits->hitNum = 0;
newAllHits->hitArrayAvailSize = SIZE_1_M;
newAllHits->readPtrArray = ( ReadPtr * ) malloc ( sizeof ( ReadPtr ) * SIZE_1_M );
newAllHits->readNum = 0;