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BGS-IO.cpp
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BGS-IO.cpp
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/*
*
* BGS-IO.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 "BGS-IO.h"
// mapping score
// dimension 1: # of mismatches (i.e. 0, 1, 2, 3, 4) OR
// difference % from the full DP score (i.e. 0, 1-5%, 6-10%, 11-15%, 15-20%, >20%)
// dimension 2: average mismatch quality value (i.e. 1-10, 11-20, 21-30, 31-40)
//static int mapping_score[6][4] = {{40,40,40,40},{38,37,35,34},{35,33,30,28},{30,28,25,22},{25,22,19,16},{19,16,13,10}};
// static int mapping_score_orig[6][4] = {{MAPQ_MAX,MAPQ_MAX,MAPQ_MAX,MAPQ_MAX},{MAPQ_MAX*0.875,MAPQ_MAX*0.875,MAPQ_MAX*0.85,MAPQ_MAX*0.85},{MAPQ_MAX*0.75,MAPQ_MAX*0.75,MAPQ_MAX*0.7,MAPQ_MAX*0.7},{MAPQ_MAX*0.625,MAPQ_MAX*0.625,MAPQ_MAX*0.55,MAPQ_MAX*0.55},{MAPQ_MAX*0.475,MAPQ_MAX*0.475,MAPQ_MAX*0.4,MAPQ_MAX*0.4},{MAPQ_MAX*0.325,MAPQ_MAX*0.325,MAPQ_MAX*0.25,MAPQ_MAX*0.25}};
static double mapping_score[6][2] = {{1.0, 1.0}, {0.875, 0.85}, {0.75, 0.7}, {0.625, 0.55}, {0.475, 0.4}, {0.325, 0.25}};
//===========================================================//
// The following is for the updated MAPQ scoring function //
// for single-end reads for DP module (Date: Oct 19, 2012) //
//===========================================================//
// The penality score when consideration of the average quality value in mismatch positions
static float penalty_score_avg_mis_qual[41] = {3, 2.85, 2.71, 2.57, 2.43, 2.3, 2.17, 2.04, 1.92, 1.8, 1.69, 1.58, 1.47, 1.37, 1.27, 1.17, 1.08, 0.99, 0.91, 0.83, 0.75, 0.68, 0.61, 0.54, 0.48, 0.42, 0.37, 0.32, 0.27, 0.23, 0.19, 0.15, 0.12, 0.09, 0.07, 0.05, 0.03, 0.02, 0.01, 0, 0};
// The penality ratio when consideration of X1
static float penalty_ratio_x1[101] = {1, 0.5, 0.33, 0.25, 0.2, 0.17, 0.14, 0.13, 0.11, 0.1, 0.09, 0.08, 0.08, 0.07, 0.07, 0.06, 0.06, 0.06, 0.05, 0.05, 0.05, 0.05, 0.04, 0.04, 0.04, 0.04, 0.04, 0.04, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01};
//
//Define the below parameter to output the alignment result(text position)
// on screen instead of writing into output file
//#define DEBUG_2BWT_OUTPUT_TO_SCREEN
//Define the below parameter to output the alignment result(text position)
// with the old 2BWT-Aligner format
//#define DEBUG_2BWT_OUTPUT_32_BIT
//Define the below parameter to stop cache reported SA range and text position.
// This is turned on when we are trying to obtain alignment timing only.
//#define DEBUG_2BWT_NO_OUTPUT
//Define the below parameter to skip writing the alignment result(text position)
// into disk. This is turned on when we are trying to obtain alignment timing only.
//#define DEBUG_2BWT_NO_WRITE_FILE
//Define the below parameter to skip translating the alignment result(text position).
// This is turned on when we are trying to obtain alignment timing only.
//#define DEBUG_2BWT_NO_TRANSLATION
OCC * OCCConstruct ()
{
OCC * occ = ( OCC * ) malloc ( sizeof ( OCC ) );
SAMOccurrenceConstruct ( occ );
occ->occPositionCacheCount = 0;
return occ;
}
void OCCFree ( OCC * occ )
{
SAMOccurrenceDestruct ( occ );
free ( occ );
}
unsigned int OCCWriteOutputHeader ( HSP * hsp, FILE * outFilePtr,
unsigned int maxReadLength,
unsigned int numOfReads,
int outputFormat )
{
unsigned int * ambiguityMap = hsp->ambiguityMap;
Translate * translate = hsp->translate;
unsigned int tp, approxIndex, approxValue;
unsigned int outputVersion = OCC_OUTPUT_FORMAT;
unsigned int writtenByteCount = 0;
int i;
switch ( outputFormat )
{
case SRA_OUTPUT_FORMAT_SAM_API:
//Ad-hoc writing header is not supported by API
break;
case SRA_OUTPUT_FORMAT_SAM:
fprintf ( outFilePtr, "@HD\tVN:1.4\tSO:unsorted\n" );
for ( i = 0; i < hsp->numOfSeq; i++ )
{
int j;
for ( j = 0; j < 255; j++ )
{
if ( hsp->annotation[i].text[j] == '\0' ||
hsp->annotation[i].text[j] == ' ' ||
hsp->annotation[i].text[j] == '\t' ||
hsp->annotation[i].text[j] == '\r' ||
hsp->annotation[i].text[j] == '\n' )
{
break;
}
}
hsp->annotation[i].text[j] = '\0';
tp = hsp->seqActualOffset[i].endPos - hsp->seqActualOffset[i].startPos + maxReadLength;
fprintf ( outFilePtr, "@SQ\tSN:%s\tLN:%u\n", hsp->annotation[i].text, tp );
}
fprintf ( outFilePtr, "@PG\tID:%s\tVN:v%d.%d.%d (%s)\n", PROJECT_NAME, PROJECT_MAJOR, PROJECT_MINOR, PROJECT_REV, PROJECT_SPECIAL );
break;
case SRA_OUTPUT_FORMAT_PLAIN:
#ifndef SKIP_PLAIN_HEADER
fprintf ( outFilePtr, "SOAP3 Plain Output File\n" );
fprintf ( outFilePtr, "========================\n" );
fprintf ( outFilePtr, "Read# ChromId# Offset Strand #Mismatch\n" );
#endif
break;
//Implicit case SRA_OUTPUT_FORMAT_DEFAULT:
default:
fwrite ( & ( outputVersion ), sizeof ( int ), 1, outFilePtr );
writtenByteCount += sizeof ( int );
fwrite ( & ( maxReadLength ), sizeof ( int ), 1, outFilePtr );
writtenByteCount += sizeof ( int );
fwrite ( & ( numOfReads ), sizeof ( int ), 1, outFilePtr );
writtenByteCount += sizeof ( int );
fwrite ( & ( hsp->numOfSeq ), sizeof ( unsigned int ), 1, outFilePtr );
writtenByteCount += sizeof ( unsigned int );
for ( i = 0; i < hsp->numOfSeq; i++ )
{
fwrite ( &hsp->annotation[i].gi, sizeof ( int ), 1, outFilePtr );
writtenByteCount += sizeof ( int );
fwrite ( &hsp->annotation[i].text, sizeof ( char ) * ( MAX_SEQ_NAME_LENGTH + 1 ), 1, outFilePtr );
writtenByteCount += sizeof ( char ) * ( MAX_SEQ_NAME_LENGTH + 1 );
tp = hsp->seqOffset[i].endPos;
approxIndex = tp >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = ambiguityMap[approxIndex];
while ( translate[approxValue].startPos > tp )
{
approxValue--;
}
tp -= translate[approxValue].correction;
fwrite ( &tp, sizeof ( unsigned int ), 1, outFilePtr );
writtenByteCount += sizeof ( unsigned int );
}
// cx Header? I don't know if we need to change this function
// have HSP
}
return writtenByteCount;
}
void AssignCigarStrToSAMIU ( bam1_t * samAlgnmt, int * curSize,
char * cigar_string )
{
char operCode[256];
operCode['M'] = 0; // match or mismatch
operCode['I'] = 1; // insertion to the reference
operCode['D'] = 2; // deletion from the reference
operCode['S'] = 4; // soft clipping
samAlgnmt->core.n_cigar = 0;
int num = 0;
for ( int i = 0; i < strlen ( cigar_string ); i++ )
{
if ( cigar_string[i] >= '0' && cigar_string[i] <= '9' )
{
num = num * 10 + cigar_string[i] - '0';
}
else if ( num > 0 )
{
SAMIUint8ConcatUint32 ( samAlgnmt->data, curSize, num << BAM_CIGAR_SHIFT | operCode[cigar_string[i]] ); //CIGAR
samAlgnmt->core.n_cigar++; //SAM: number of CIGAR operations
num = 0;
}
}
}
void OCCFlushCachePlain ( OCC * occ, HSP * hsp, FILE * outFilePtr, SRAQueryInput * qInput )
{
char strandStr[4] = "?+-";
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
OCCPositionCache lastDelimEntry;
if ( occ->occPositionCacheCount > 0 )
{
// ALERT: THIS PART IS NOT 64-BIT COMPATIBLE.
unsigned long long j;
unsigned int tp;
unsigned int approxIndex, approxValue;
unsigned long long k = 0;
j = 0;
for ( k = 0; k < occ->occPositionCacheCount; k++ )
{
if ( occ->occPositionCache[j].ChromId == OCC_CONST_ALIGNMENT_HEADER )
{
lastDelimEntry.ChromId = occ->occPositionCache[j].ChromId;
lastDelimEntry.occMismatch = occ->occPositionCache[j].occMismatch;
lastDelimEntry.ReadStrand = occ->occPositionCache[j].ReadStrand;
lastDelimEntry.tp = occ->occPositionCache[j].tp;
}
else if ( occ->occPositionCache[j].ChromId == OCC_CONST_NO_ALIGNMENT )
{
}
else if ( occ->occPositionCache[j].ReadStrand != 0 )
{
tp = ( unsigned int ) occ->occPositionCache[j].tp;
#ifndef DEBUG_2BWT_NO_TRANSLATION
approxIndex = tp >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > tp )
{
approxValue--;
}
tp -= occTranslate[approxValue].correction;
// cx non-DP translation check tp
// have HSP
// ADD_CX
unsigned int pacPos = ( unsigned int ) occ->occPositionCache[j].tp;
unsigned int chrEndPos = hsp->seqOffset[occTranslate[approxValue].chrID - 1].endPos;
int readLength = occ->occPositionCache[j].len;
char * buffer;
int correctedChrID;
unsigned int correctedChrPos;
if ( 0 /*BoundaryCheck(pacPos, occTranslate[approxValue].chrID, chrEndPos, readLength, hsp, correctedChrID, buffer)*/ )
{
fprintf ( outFilePtr, "AAA+ %llu %u ???? %c ? %s\n", lastDelimEntry.tp, correctedChrID, /*( unsigned long long ) tp,*/ strandStr[occ->occPositionCache[j].ReadStrand], buffer );
free ( buffer );
}
else
{
#endif
#ifdef DEBUG_2BWT_NO_TRANSLATION
occ->occPositionCacheToDisk[j].cell[1] = 0;
#endif
#ifdef DEBUG_2BWT_OUTPUT_TO_SCREEN
printf ( "[OCCFlushCache] %d %d \n", occTranslate[approxValue].chrID, tp );
#endif
fprintf ( outFilePtr, "AAA %llu %u %llu %c %d\n", lastDelimEntry.tp, occTranslate[approxValue].chrID, ( unsigned long long ) tp, strandStr[occ->occPositionCache[j].ReadStrand], occ->occPositionCache[j].occMismatch );
}
}
j++;
}
}
occ->occPositionCache[0].ChromId = lastDelimEntry.ChromId;
occ->occPositionCache[0].occMismatch = lastDelimEntry.occMismatch;
occ->occPositionCache[0].ReadStrand = lastDelimEntry.ReadStrand;
occ->occPositionCache[0].tp = lastDelimEntry.tp;
occ->occPositionCache[0].len = lastDelimEntry.len;
occ->occPositionCacheCount = 1;
}
void OCCFlushCachePlainDP ( OCC * occ, HSP * hsp, FILE * outFilePtr )
{
char strandStr[4] = "?+-";
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
OCCPositionCache lastDelimEntry;
if ( occ->occPositionCacheCount > 0 )
{
// ALERT: THIS PART IS NOT 64-BIT COMPATIBLE.
unsigned long long j;
unsigned int tp;
unsigned int approxIndex, approxValue;
unsigned long long k = 0;
j = 0;
for ( k = 0; k < occ->occPositionCacheCount; k++ )
{
if ( occ->occPositionCache[j].ChromId == OCC_CONST_ALIGNMENT_HEADER )
{
lastDelimEntry.ChromId = occ->occPositionCache[j].ChromId;
lastDelimEntry.occMismatch = occ->occPositionCache[j].occMismatch;
lastDelimEntry.ReadStrand = occ->occPositionCache[j].ReadStrand;
lastDelimEntry.tp = occ->occPositionCache[j].tp;
lastDelimEntry.resultSource = occ->occPositionCache[j].resultSource;
lastDelimEntry.cigarString = occ->occPositionCache[j].cigarString;
lastDelimEntry.len = occ->occPositionCache[j].len;
}
else if ( occ->occPositionCache[j].ChromId == OCC_CONST_NO_ALIGNMENT )
{
}
else if ( occ->occPositionCache[j].ReadStrand != 0 )
{
tp = ( unsigned int ) occ->occPositionCache[j].tp;
#ifndef DEBUG_2BWT_NO_TRANSLATION
approxIndex = tp >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > tp )
{
approxValue--;
}
tp -= occTranslate[approxValue].correction;
// cx both non-DP and DP results (occ->occPositionCache[j].resultSource = 1). check tp
// have HSP
#endif
// ADD_CX .... handle non-DP alignment only
if ( occ->occPositionCache[j].resultSource == 0 )
{
}
else // handle DP alignment here
{
}
#ifdef DEBUG_2BWT_NO_TRANSLATION
occ->occPositionCacheToDisk[j].cell[1] = 0;
#endif
#ifdef DEBUG_2BWT_OUTPUT_TO_SCREEN
printf ( "[OCCFlushCache] %d %d \n", occTranslate[approxValue].chrID, tp );
#endif
if ( occ->occPositionCache[j].resultSource == 0 )
{
// the result is from SOAP3
unsigned int pacPos = ( unsigned int ) occ->occPositionCache[j].tp;
unsigned int chrEndPos = hsp->seqOffset[occTranslate[approxValue].chrID - 1].endPos;
int readLength = occ->occPositionCache[j].len;
char * buffer;
int correctedChrID;
unsigned int correctedChrPos;
if ( 0 /*BoundaryCheck(pacPos, occTranslate[approxValue].chrID, chrEndPos, readLength, hsp, correctedChrID, buffer) */ )
{
fprintf ( outFilePtr, "XXX+ %llu %u ???? %c ? %d %s\n", lastDelimEntry.tp, correctedChrID, /*( unsigned long long ) tp,*/ strandStr[occ->occPositionCache[j].ReadStrand], occ->occPositionCache[j].resultSource, buffer );
free ( buffer );
}
else
{
fprintf ( outFilePtr, "XXX %llu %u %llu %c %d %d %dM\n", lastDelimEntry.tp, occTranslate[approxValue].chrID, ( unsigned long long ) tp, strandStr[occ->occPositionCache[j].ReadStrand], occ->occPositionCache[j].occMismatch, occ->occPositionCache[j].resultSource, occ->occPositionCache[j].len );
}
}
else
{
// the result is from DP
unsigned int pacPos = ( unsigned int ) occ->occPositionCache[j].tp;
unsigned int chrEndPos = hsp->seqOffset[occTranslate[approxValue].chrID - 1].endPos;
int readLength = occ->occPositionCache[j].len;
int correctedChrID;
unsigned int correctedChrPos;
char * buffer;
if ( 0 /*BoundaryCheckDP(pacPos, occTranslate[approxValue].chrID, chrEndPos, readLength, occ->occPositionCache[j].cigarString,
hsp, correctedChrID, buffer) */ )
{
fprintf ( outFilePtr, "YYY+ %llu %u ???? %c ? %d %s\n", lastDelimEntry.tp, correctedChrID, strandStr[occ->occPositionCache[j].ReadStrand], occ->occPositionCache[j].resultSource, buffer );
free ( buffer );
}
else
{
fprintf ( outFilePtr, "YYY %llu %u %llu %c %d %d %s\n", lastDelimEntry.tp, occTranslate[approxValue].chrID, ( unsigned long long ) tp, strandStr[occ->occPositionCache[j].ReadStrand], occ->occPositionCache[j].occMismatch, occ->occPositionCache[j].resultSource, occ->occPositionCache[j].cigarString );
}
}
}
j++;
}
}
occ->occPositionCache[0].ChromId = lastDelimEntry.ChromId;
occ->occPositionCache[0].occMismatch = lastDelimEntry.occMismatch;
occ->occPositionCache[0].ReadStrand = lastDelimEntry.ReadStrand;
occ->occPositionCache[0].tp = lastDelimEntry.tp;
occ->occPositionCache[0].resultSource = lastDelimEntry.resultSource;
occ->occPositionCache[0].cigarString = lastDelimEntry.cigarString;
occ->occPositionCache[0].len = lastDelimEntry.len;
occ->occPositionCacheCount = 1;
}
// binary output. ignore.
void OCCFlushCacheDefault ( OCC * occ, HSP * hsp, FILE * outFilePtr )
{
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
if ( occ->occPositionCacheCount > 0 )
{
// ALERT: THIS PART IS NOT 64-BIT COMPATIBLE.
unsigned long long j;
unsigned int tp;
unsigned int approxIndex, approxValue;
unsigned long long k = 0;
j = 0;
for ( k = 0; k < occ->occPositionCacheCount; k++ )
{
if ( occ->occPositionCache[j].ChromId == OCC_CONST_ALIGNMENT_HEADER )
{
#ifdef DEBUG_2BWT_OUTPUT_32_BIT
( * ( unsigned int * ) & ( occ->occPositionCacheToDisk[j].cell[1] ) ) = ( unsigned int ) occ->occPositionCache[j].tp;
occ->occPositionCacheToDisk[j].cell[0] = 0;
#endif
#ifndef DEBUG_2BWT_OUTPUT_32_BIT
( * ( unsigned long long * ) & ( occ->occPositionCacheToDisk[j].cell[3] ) ) = ( unsigned long long ) occ->occPositionCache[j].tp;
occ->occPositionCacheToDisk[j].cell[1] = 0;
occ->occPositionCacheToDisk[j].cell[0] = 0;
#endif
}
else if ( occ->occPositionCache[j].ChromId == OCC_CONST_NO_ALIGNMENT )
{
}
else
{
tp = ( unsigned int ) occ->occPositionCache[j].tp;
#ifndef DEBUG_2BWT_NO_TRANSLATION
approxIndex = tp >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > tp )
{
approxValue--;
}
tp -= occTranslate[approxValue].correction;
// cx non-DP??? check tp
// have HSP
#endif
#ifdef DEBUG_2BWT_NO_TRANSLATION
#ifdef DEBUG_2BWT_OUTPUT_32_BIT
occ->occPositionCacheToDisk[j].cell[0] = 0;
#endif
#ifndef DEBUG_2BWT_OUTPUT_32_BIT
occ->occPositionCacheToDisk[j].cell[1] = 0;
#endif
#endif
#ifdef DEBUG_2BWT_OUTPUT_TO_SCREEN
printf ( "[OCCFlushCache] %d %d \n", occTranslate[approxValue].chrID, tp );
#endif
#ifdef DEBUG_2BWT_OUTPUT_32_BIT
( * ( unsigned int * ) & ( occ->occPositionCacheToDisk[j].cell[1] ) ) = ( unsigned int ) tp;
occ->occPositionCacheToDisk[j].cell[0] = occTranslate[approxValue].chrID;
#endif
#ifndef DEBUG_2BWT_OUTPUT_32_BIT
( * ( unsigned long long * ) & ( occ->occPositionCacheToDisk[j].cell[3] ) ) = ( unsigned long long ) tp;
occ->occPositionCacheToDisk[j].cell[0] = occ->occPositionCache[j].ReadStrand;
occ->occPositionCacheToDisk[j].cell[1] = occTranslate[approxValue].chrID;
#endif
}
j++;
}
#ifndef DEBUG_2BWT_NO_WRITE_FILE
fwrite ( occ->occPositionCacheToDisk, sizeof ( OCCPositionCacheToDisk ) *occ->occPositionCacheCount, 1, outFilePtr );
#endif
}
occ->occPositionCacheCount = 0;
}
/*
void OCCDirectWritePairUnmapSAM ( SRAQueryInput * qInput, SRAOccurrence * sraOcc, int isFirst )
{
SRASetting * qSetting = qInput->QuerySetting;
// int OutFileFormat = qSetting->OutFileFormat;
FILE * outFilePtr = qSetting->OutFilePtr;
SRAQueryInfo * qInfo = qInput->QueryInfo;
SRAIndex * aIndex = qInput->AlgnmtIndex;
HSP * hsp = aIndex->hsp;
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
// unsigned long long j=0, k=0;
unsigned long long ambPosition;
unsigned long long tp;
unsigned int correctPosition;
unsigned int approxIndex, approxValue;
unsigned long long occCount = 0;
// ATTENTION: THIS PART IS NOT 64-BIT COMPATIBLE.
{
ambPosition = sraOcc->ambPosition;
tp = ambPosition;
correctPosition = ambPosition;
approxIndex = ambPosition >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > ambPosition )
{
approxValue--;
}
correctPosition -= occTranslate[approxValue].correction;
tp = correctPosition;
//QNAME FLAG RNAME POS
//MAPQ CIGAR RNEXT PNEXT TLEN
//SEQ QUAL
unsigned int samFlag = 0;
samFlag |= SAM_FLAG_MATE_UNMAPPED;
samFlag |= SAM_FLAG_FIRST_IN_PAIR * isFirst;
samFlag |= SAM_FLAG_SECOND_IN_PAIR * ( 1 - isFirst );
if ( sraOcc->strand == QUERY_NEG_STRAND )
{
samFlag |= SAM_FLAG_READ_ALGNMT_STRAND * isFirst;
}
samFlag |= isFirst *
fprintf ( outFilePtr, "%s\t%u\t%s\t%llu\t%d\t%lluM\t%s\t%llu\t%d\t",
qInfo->ReadName, //QNAME
samFlag, //FLAG
hsp->annotation[occTranslate[approxValue].chrID - 1].text, //RNAME
tp, //POS
SAM_MAPQ_UNAVAILABLE, //MAPQ
qInfo->ReadLength, //CIGAR
"*", //MRNM
0LL, //MPOS
0 //ISIZE
);
int i;
for ( i = 0; i < qInfo->ReadLength; i++ )
{
fprintf ( outFilePtr, "%c", dnaChar[qInfo->ReadCode[i]] ); //SEQ
}
fprintf ( outFilePtr, "\t" );
for ( i = 0; i < qInfo->ReadLength; i++ )
{
fprintf ( outFilePtr, "%c", 33 ); //QUAL
}
fprintf ( outFilePtr, "\n" );
occCount++;
}
}
void OCCDirectWritePairOccSAM ( SRAQueryInput * qInput, PEPairs * pePair )
{
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
// int OutFileFormat = qSetting->OutFileFormat;
SRAQueryInfo * qInfo = qInput->QueryInfo;
FILE * outFilePtr = qSetting->OutFilePtr;
HSP * hsp = aIndex->hsp;
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
// unsigned long long j=0, k=0;
unsigned long long ambPosition;
unsigned long long tp_1, tp_2;
char chr_1, chr_2;
unsigned int correctPosition;
unsigned int approxIndex, approxValue;
// unsigned long long occCount = 0;
char * mateChar;
char equalChr[3] = "=";
// ATTENTION: THIS PART IS NOT 64-BIT COMPATIBLE.
{
ambPosition = pePair->algnmt_1;
tp_1 = ambPosition;
correctPosition = ambPosition;
approxIndex = ambPosition >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > ambPosition )
{
approxValue--;
}
correctPosition -= occTranslate[approxValue].correction;
tp_1 = correctPosition;
chr_1 = occTranslate[approxValue].chrID - 1;
}
{
ambPosition = pePair->algnmt_2;
tp_2 = ambPosition;
correctPosition = ambPosition;
approxIndex = ambPosition >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > ambPosition )
{
approxValue--;
}
correctPosition -= occTranslate[approxValue].correction;
tp_2 = correctPosition;
chr_2 = occTranslate[approxValue].chrID - 1;
}
if ( chr_1 == chr_2 ) { mateChar = equalChr; }
else { mateChar = hsp->annotation[chr_2].text; }
unsigned int samFlag = 0;
samFlag |= SAM_FLAG_PROPER_PAIR;
samFlag |= SAM_FLAG_FIRST_IN_PAIR;
if ( pePair->strand_1 == QUERY_NEG_STRAND )
{
samFlag |= SAM_FLAG_READ_ALGNMT_STRAND;
}
if ( pePair->strand_2 == QUERY_NEG_STRAND )
{
samFlag |= SAM_FLAG_MATE_ALGNMT_STRAND;
}
//QNAME FLAG RNAME POS
//MAPQ CIGAR RNEXT PNEXT TLEN
//SEQ QUAL
fprintf ( outFilePtr, "%s\t%u\t%s\t%llu\t%d\t%lluM\t%s\t%llu\t%d\t",
qInfo->ReadName, //QNAME
samFlag, //FLAG
hsp->annotation[chr_1].text, //RNAME
tp_1, //POS
SAM_MAPQ_UNAVAILABLE, //MAPQ (unavailable)
qInfo->ReadLength, //CIGAR
mateChar, //MRNM
tp_2, //MPOS
pePair->insertion //ISIZE (unavailable in single-end)
);
int i;
for ( i = 0; i < qInfo->ReadLength; i++ )
{
fprintf ( outFilePtr, "%c", dnaChar[qInfo->ReadCode[i]] ); //SEQ
}
fprintf ( outFilePtr, "\t" );
for ( i = 0; i < qInfo->ReadLength; i++ )
{
fprintf ( outFilePtr, "%c", 33 ); //QUAL
}
fprintf ( outFilePtr, "\n" );
}
*/
void OCCFlushCacheSAM ( SRAQueryInput * qInput )
{
SRAQueryInfo * qInfo = qInput->QueryInfo;
SRASetting * qSetting = qInput->QuerySetting;
// int OutFileFormat = qSetting->OutFileFormat;
FILE * outFilePtr = qSetting->OutFilePtr;
SRAIndex * aIndex = qInput->AlgnmtIndex;
OCC * occ = qSetting->occ;
HSP * hsp = aIndex->hsp;
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
unsigned long long j = 0, k = 0;
unsigned long long ambPosition;
unsigned long long tp;
unsigned int correctPosition;
unsigned int approxIndex, approxValue;
unsigned long long occCount = 0;
for ( k = 0; k < occ->occPositionCacheCount; k++ )
{
if ( occ->occPositionCache[j].ChromId == OCC_CONST_ALIGNMENT_HEADER )
{
}
else if ( occ->occPositionCache[j].ChromId == OCC_CONST_NO_ALIGNMENT )
{
}
else
{
// ATTENTION: THIS PART IS NOT 64-BIT COMPATIBLE.
ambPosition = occ->occPositionCache[j].tp;
tp = ambPosition;
correctPosition = ambPosition;
approxIndex = ambPosition >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > ambPosition )
{
approxValue--;
}
correctPosition -= occTranslate[approxValue].correction;
tp = correctPosition;
// cx non-DP, check tp
// have HSP as local variable
unsigned int samFlag = 0;
if ( occ->occPositionCache[j].ReadStrand == QUERY_NEG_STRAND )
{
samFlag |= SAM_FLAG_READ_ALGNMT_STRAND;
}
//QNAME FLAG RNAME POS
//MAPQ CIGAR RNEXT PNEXT TLEN
//SEQ QUAL
fprintf ( outFilePtr, "%s\t%u\t%s\t%llu\t%d\t%lluM\t%s\t%llu\t%d\t",
qInfo->ReadName, //QNAME
samFlag, //FLAG
hsp->annotation[occTranslate[approxValue].chrID - 1].text, //RNAME
tp, //POS
SAM_MAPQ_UNAVAILABLE, //MAPQ (unavailable)
qInfo->ReadLength, //CIGAR
"*", //MRNM (unavailable in single-end)
0LL, //MPOS (unavailable in single-end)
0 //ISIZE (unavailable in single-end)
);
int i;
for ( i = 0; i < qInfo->ReadLength; i++ )
{
fprintf ( outFilePtr, "%c", dnaChar[qInfo->ReadCode[i]] ); //SEQ
}
fprintf ( outFilePtr, "\t" );
for ( i = 0; i < qInfo->ReadLength; i++ )
{
fprintf ( outFilePtr, "%c", 33 ); //QUAL
}
fprintf ( outFilePtr, "\n" );
occCount++;
}
j++;
}
if ( occCount == 0 )
{
unsigned int samFlag = 0;
samFlag |= SAM_FLAG_READ_UNMAPPED;
fprintf ( outFilePtr, "%s\t%u\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%s\t%s\n",
qInfo->ReadName, //QNAME
samFlag, //FLAG
"*", //RNAME
0LL, //POS
0, //MAPQ
"*", //CIGAR
"*", //MRNM
0LL, //MPOS
0, //ISIZE
"*", //SEQ
"*" //QUAL
);
}
qSetting->writtenCacheCount++;
occ->occPositionCacheCount = 0;
}
void OCCFlushCacheSAMAPI ( SRAQueryInput * qInput )
{
// fprintf(stderr,"OCCFlushCacheSAMAPI\n");
SRAQueryInfo * qInfo = qInput->QueryInfo;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
// int OutFileFormat = qSetting->OutFileFormat;
// FILE * outFilePtr = qSetting->OutFilePtr;
OCC * occ = qSetting->occ;
HSP * hsp = aIndex->hsp;
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
samfile_t * samFilePtr = qSetting->SAMOutFilePtr;
bam1_t * samAlgnmt = & ( occ->SAMOutBuffer );
unsigned long long i = 0, j = 0, k = 0;
unsigned long long ambPosition;
unsigned long long tp;
unsigned int correctPosition;
unsigned int approxIndex, approxValue;
//Assuming the answer being handled by OCCFlushCacheSAMAPI are all answers of qInput
// Each occurrences reported by SAM_API will share the following aux data.
//----------------------------------------------------------------------------------------------------------------------------
samAlgnmt->core.bin = bam_reg2bin ( 0, 0 ); //SAM: bin calculated by bam_reg2bin()
samAlgnmt->core.n_cigar = 1; //SAM: number of CIGAR operations
samAlgnmt->core.l_qseq = qInfo->ReadLength; //SAM: length of the query sequence (read)
samAlgnmt->core.l_qname = strlen ( qInfo->ReadName ) + 1; //SAM: length of the query name
samAlgnmt->core.mtid = -1;
samAlgnmt->core.mpos = -1;
samAlgnmt->core.isize = 0;
samAlgnmt->l_aux = 0;
samAlgnmt->data_len = 0;
samAlgnmt->m_data = SAM_MDATA_SIZE;
SAMIUint8ConcatString ( samAlgnmt->data, & ( samAlgnmt->data_len ), qInfo->ReadName, strlen ( qInfo->ReadName ) + 1 ); //Name
SAMIUint8ConcatUint32 ( samAlgnmt->data, & ( samAlgnmt->data_len ), qInfo->ReadLength << BAM_CIGAR_SHIFT ); //CIGAR
for ( i = 0; i < qInfo->ReadLength / 2; i++ ) //Read
{
unsigned char biChar = 0;
biChar |= bam_nt16_table[dnaChar[qInfo->ReadCode[i * 2]]] << 4;
biChar |= bam_nt16_table[dnaChar[qInfo->ReadCode[i * 2 + 1]]];
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), biChar );
}
if ( qInfo->ReadLength % 2 == 1 )
{
uint8_t biChar = bam_nt16_table[dnaChar[qInfo->ReadCode[qInfo->ReadLength - 1]]] << 4;
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), biChar );
}
for ( i = 0; i < qInfo->ReadLength; i++ ) //Quality
{
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), 0xff );
}
unsigned int auxStart = samAlgnmt->data_len;
//SAMIUint8ConcatString(samAlgnmt->data,&(samAlgnmt->data_len),"XAZTESTING",11);
samAlgnmt->l_aux += samAlgnmt->data_len - auxStart;
//----------------------------------------------------------------------------------------------------------------------------
unsigned long long occCount = 0;
for ( k = 0; k < occ->occPositionCacheCount; k++ )
{
if ( occ->occPositionCache[j].ChromId == OCC_CONST_ALIGNMENT_HEADER )
{
}
else if ( occ->occPositionCache[j].ChromId == OCC_CONST_NO_ALIGNMENT )
{
unsigned int samFlag = 0;
samFlag |= SAM_FLAG_READ_UNMAPPED;
// ----------------------> |
samAlgnmt->core.tid = -1; //SAM: chromosome ID, defined by bam_header_t
samAlgnmt->core.pos = -1; //SAM: 0-based leftmost coordinate4
samAlgnmt->core.qual = 0; //SAM: mapping quality
samAlgnmt->core.flag = samFlag; //SAM: bitwise flag
samwrite ( samFilePtr, samAlgnmt );
// ----------------------> |
}
else
{
// ATTENTION: THIS PART IS NOT 64-BIT COMPATIBLE.
ambPosition = occ->occPositionCache[j].tp;
tp = ambPosition;
correctPosition = ambPosition;
approxIndex = ambPosition >> GRID_SAMPLING_FACTOR_2_POWER;
approxValue = occAmbiguityMap[approxIndex];
while ( occTranslate[approxValue].startPos > ambPosition )
{
approxValue--;
}
correctPosition -= occTranslate[approxValue].correction;
tp = correctPosition;
// cx non-DP, check tp
// have HSP
// modify CIGAR string seems hard, probably need call SAMIUintxxxxx functions, or AssignCIGARStrToSAMIU
unsigned int samFlag = 0;
if ( occ->occPositionCache[j].ReadStrand == QUERY_NEG_STRAND )
{
samFlag |= SAM_FLAG_READ_ALGNMT_STRAND;
}
// ----------------------> |
samAlgnmt->core.tid = occTranslate[approxValue].chrID - 1; //SAM: chromosome ID, defined by bam_header_t
samAlgnmt->core.pos = tp - 1; //SAM: 0-based leftmost coordinate
samAlgnmt->core.qual = SAM_MAPQ_UNAVAILABLE; //SAM: mapping quality
samAlgnmt->core.flag = samFlag; //SAM: bitwise flag
samwrite ( samFilePtr, samAlgnmt );
// ----------------------> |
occCount++;
}
j++;
}
qSetting->writtenCacheCount++;
occ->occPositionCacheCount = 0;
}
void OCCFlushCacheSAMAPIDP ( SRAQueryInput * qInput )
{
// fprintf(stderr,"OCCFlushCacheSAMAPIDP\n");
SRAQueryInfo * qInfo = qInput->QueryInfo;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
// int OutFileFormat = qSetting->OutFileFormat;
// FILE * outFilePtr = qSetting->OutFilePtr;
OCC * occ = qSetting->occ;
HSP * hsp = aIndex->hsp;
Translate * occTranslate = hsp->translate;
unsigned int * occAmbiguityMap = hsp->ambiguityMap;
samfile_t * samFilePtr = qSetting->SAMOutFilePtr;
bam1_t * samAlgnmt = & ( occ->SAMOutBuffer );
unsigned long long i = 0, j = 0, k = 0;
unsigned long long ambPosition;
unsigned long long tp;
unsigned int correctPosition;
unsigned int approxIndex, approxValue;
unsigned long long occCount = 0;
for ( k = 0; k < occ->occPositionCacheCount; k++ )
{
if ( occ->occPositionCache[j].ChromId == OCC_CONST_ALIGNMENT_HEADER )
{
}
else if ( occ->occPositionCache[j].ChromId == OCC_CONST_NO_ALIGNMENT )
{
//Assuming the answer being handled by OCCFlushCacheSAMAPI are all answers of qInput
// Each occurrences reported by SAM_API will share the following aux data.
//----------------------------------------------------------------------------------------------------------------------------
samAlgnmt->core.bin = bam_reg2bin ( 0, 0 ); //SAM: bin calculated by bam_reg2bin()
samAlgnmt->core.n_cigar = 1; //SAM: number of CIGAR operations
samAlgnmt->core.l_qseq = qInfo->ReadLength; //SAM: length of the query sequence (read)
samAlgnmt->core.l_qname = strlen ( qInfo->ReadName ) + 1; //SAM: length of the query name
samAlgnmt->core.mtid = -1;
samAlgnmt->core.mpos = -1;
samAlgnmt->core.isize = 0;
samAlgnmt->l_aux = 0;
samAlgnmt->data_len = 0;
samAlgnmt->m_data = SAM_MDATA_SIZE;
SAMIUint8ConcatString ( samAlgnmt->data, & ( samAlgnmt->data_len ), qInfo->ReadName, strlen ( qInfo->ReadName ) + 1 ); //Name
SAMIUint8ConcatUint32 ( samAlgnmt->data, & ( samAlgnmt->data_len ), qInfo->ReadLength << BAM_CIGAR_SHIFT ); //CIGAR
for ( i = 0; i < qInfo->ReadLength / 2; i++ ) //Read
{
unsigned char biChar = 0;
biChar |= bam_nt16_table[dnaChar[qInfo->ReadCode[i * 2]]] << 4;
biChar |= bam_nt16_table[dnaChar[qInfo->ReadCode[i * 2 + 1]]];
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), biChar );
}
if ( qInfo->ReadLength % 2 == 1 )
{
uint8_t biChar = bam_nt16_table[dnaChar[qInfo->ReadCode[qInfo->ReadLength - 1]]] << 4;
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), biChar );
}
for ( i = 0; i < qInfo->ReadLength; i++ ) //Quality
{
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), 0xff );
}
unsigned int auxStart = samAlgnmt->data_len;
//SAMIUint8ConcatString(samAlgnmt->data,&(samAlgnmt->data_len),"XAZTESTING",11);
samAlgnmt->l_aux += samAlgnmt->data_len - auxStart;
//----------------------------------------------------------------------------------------------------------------------------
unsigned int samFlag = 0;
samFlag |= SAM_FLAG_READ_UNMAPPED;
// ----------------------> |
samAlgnmt->core.tid = -1; //SAM: chromosome ID, defined by bam_header_t
samAlgnmt->core.pos = -1; //SAM: 0-based leftmost coordinate4
samAlgnmt->core.qual = 0; //SAM: mapping quality
samAlgnmt->core.flag = samFlag; //SAM: bitwise flag
samwrite ( samFilePtr, samAlgnmt );
// ----------------------> |
}
else
{
//Assuming the answer being handled by OCCFlushCacheSAMAPI are all answers of qInput
// Each occurrences reported by SAM_API will share the following aux data.
//----------------------------------------------------------------------------------------------------------------------------
samAlgnmt->core.bin = bam_reg2bin ( 0, 0 ); //SAM: bin calculated by bam_reg2bin()
samAlgnmt->core.n_cigar = 1; //SAM: number of CIGAR operations
samAlgnmt->core.l_qseq = qInfo->ReadLength; //SAM: length of the query sequence (read)
samAlgnmt->core.l_qname = strlen ( qInfo->ReadName ) + 1; //SAM: length of the query name
samAlgnmt->core.mtid = -1;
samAlgnmt->core.mpos = -1;
samAlgnmt->core.isize = 0;
samAlgnmt->l_aux = 0;
samAlgnmt->data_len = 0;
samAlgnmt->m_data = SAM_MDATA_SIZE;
SAMIUint8ConcatString ( samAlgnmt->data, & ( samAlgnmt->data_len ), qInfo->ReadName, strlen ( qInfo->ReadName ) + 1 ); //Name
AssignCigarStrToSAMIU ( samAlgnmt, & ( samAlgnmt->data_len ), occ->occPositionCache[j].cigarString );
for ( i = 0; i < qInfo->ReadLength / 2; i++ ) //Read
{
unsigned char biChar = 0;
biChar |= bam_nt16_table[dnaChar[qInfo->ReadCode[i * 2]]] << 4;
biChar |= bam_nt16_table[dnaChar[qInfo->ReadCode[i * 2 + 1]]];
SAMIUint8ConcatUint8 ( samAlgnmt->data, & ( samAlgnmt->data_len ), biChar );
}