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QueryParser.cpp
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QueryParser.cpp
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/*
*
* QueryParser.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 "QueryParser.h"
// This function is to load reads for BAM format
int loadBAMReads ( bamFile bamQueryFile, bam_header_t * bamHeader, bam1_t * b, unsigned char * charMap,
uint * queries, uint * readLengths, uint * readIDs, char * upkdQualities, char * upkdQueryNames, uint maxReadLength, uint maxNumQueries,
uint wordPerQuery, int qualityConstant, int maxLenReadName )
{
uint * queryPtr = queries;
ullint queriesRead = 0;
uint currentWord = 0;
uint offset = 0;
uint bits = 0;
while ( queriesRead < maxNumQueries && bam_read1 ( bamQueryFile, b ) >= 0 )
{
// get the information of one read from BAM file
char * rec_seq = bam_format1 ( bamHeader, b );
// format: id >> flag >> chr >> pos >> mapQ >> cigar >> mateChr >> matePos >> insertSize >> seq >> qual;
int rec_len = strlen ( rec_seq );
int pos = 0;
// store the read description
int i = 0;
while ( pos < rec_len && rec_seq[pos] != '\t' )
{
if ( i < maxLenReadName - 1 )
{
upkdQueryNames[queriesRead * maxLenReadName + i] = rec_seq[pos];
i++;
}
pos++;
}
upkdQueryNames[queriesRead * maxLenReadName + i] = '\0';
// skip the spaces
while ( pos < rec_len && rec_seq[pos] == '\t' )
{ pos++; }
// get the flag
unsigned int flag = 0;
while ( pos < rec_len && rec_seq[pos] != '\t' )
{
flag = flag * 10 + ( rec_seq[pos] - '0' );
pos++;
}
// skip the spaces
while ( pos < rec_len && rec_seq[pos] == '\t' )
{ pos++; }
// skip seven columns
// i.e. chr >> pos >> mapQ >> cigar >> mateChr >> matePos >> insertSize
for ( i = 0; i < 7; i++ )
{
// skip the column
while ( pos < rec_len && rec_seq[pos] != '\t' )
{ pos++; }
// skip the spaces
while ( pos < rec_len && rec_seq[pos] == '\t' )
{ pos++; }
}
// get the length of read sequence
int seq_len = 0;
while ( pos + seq_len < rec_len && rec_seq[pos + seq_len] != '\t' )
{ seq_len++; }
// store the read sequence
currentWord = 0;
offset = 0;
int isFWD = 1;
if ( ( flag & SAM_FLAG_READ_ALGNMT_STRAND ) != 0 )
{
isFWD = 0; // reverse strand
}
if ( isFWD )
{
i = 0;
while ( i < seq_len && i < maxReadLength )
{
bits = charMap[rec_seq[pos + i]];
currentWord |= ( bits << ( offset * BIT_PER_CHAR ) );
offset++;
i++;
if ( offset == CHAR_PER_WORD )
{
*queryPtr = currentWord;
queryPtr += 32;
offset = 0;
currentWord = 0;
}
}
}
else
{
i = seq_len - 1;
while ( i >= 0 && seq_len - i <= maxReadLength )
{
bits = soap3DnaComplement[rec_seq[pos + i]];
currentWord |= ( bits << ( offset * BIT_PER_CHAR ) );
offset++;
i--;
if ( offset == CHAR_PER_WORD )
{
*queryPtr = currentWord;
queryPtr += 32;
offset = 0;
currentWord = 0;
}
}
}
pos += seq_len;
if ( offset > 0 )
{ *queryPtr = currentWord; }
readLengths[queriesRead] = ( seq_len > maxReadLength ) ? maxReadLength : seq_len;
readIDs[queriesRead] = queriesRead + 1;
// skip the spaces
while ( pos < rec_len && rec_seq[pos] == '\t' )
{ pos++; }
// store the quality values
for ( i = 0; i < readLengths[queriesRead]; i++ )
{
if ( isFWD )
{ upkdQualities[queriesRead * maxReadLength + i] = rec_seq[pos + i] - qualityConstant; }
else
{ upkdQualities[queriesRead * maxReadLength + i] = rec_seq[pos + seq_len - i - 1] - qualityConstant; }
}
queriesRead++;
queryPtr = queries + ( queriesRead / 32 * 32 * wordPerQuery + queriesRead % 32 );
free ( rec_seq );
}
return queriesRead;
}
// This function is to load the pair-end reads for at most "maxNumQueries/2" # of pairs of reads
int loadPairReadsGz2 ( gzFile queryFile, char * queryFileBuffer, gzFile queryFile2, char * queryFileBuffer2, unsigned char * charMap,
uint * queries, uint * readLengths, uint * readIDs, char * upkdQualities, char * upkdQueryNames, uint maxReadLength, uint maxNumQueries,
size_t & bufferSize, char & queryChar, uint & bufferIndex, size_t & bufferSize2, char & queryChar2, uint & bufferIndex2,
uint accumReadNum, uint wordPerQuery, int qualityConstant, char & isFastq, int maxLenReadName )
{
// for pair-ended reads
// load reads from the read file
// return how many reads are loaded
ullint queriesRead = 0;
uint currentWord = 0;
uint offset = 0;
uint bits = 0;
uint * queryPtr = queries;
int i;
uint nameCharId;
int cropped;
uint nucleoId;
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
// FOR THE FIRST READ
while ( bufferSize != 0 )
{
//Read everything before the entry point of a read, character ">"
while ( bufferSize != 0 && queryChar != '>' && queryChar != '@' )
{
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
isFastq = 0;
if ( queryChar == '@' ) {isFastq = 1;}
//Read the header of a read
if ( bufferSize == 0 ) { break; }
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
nameCharId = 0;
cropped = 0;
while ( bufferSize != 0 && queryChar != '\n' )
{
if ( queryChar == ' ' || queryChar == '\t' ) {cropped = 1;}
if ( !cropped && nameCharId < maxLenReadName - 1 )
{
upkdQueryNames[queriesRead * maxLenReadName + ( nameCharId++ )] = queryChar;
}
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
// remove "/1" or "/2" if exists
if ( nameCharId - 2 >= 0 && upkdQueryNames[queriesRead * maxLenReadName + ( nameCharId - 2 )] == '/' )
{ upkdQueryNames[queriesRead * maxLenReadName + ( nameCharId - 2 )] = '\0'; }
else
{ upkdQueryNames[queriesRead * maxLenReadName + nameCharId] = '\0'; }
//Read the pattern body of a read
if ( bufferSize == 0 ) { break; }
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
nucleoId = 0;
while ( bufferSize != 0 && queryChar != '>' && queryChar != '@' && queryChar != '+' )
{
if ( queryChar != '\n' )
{
bits = charMap[queryChar];
if ( nucleoId < maxReadLength )
{
// upkdQueries[queriesRead*maxReadLength+nucleoId]=bits;
currentWord |= ( bits << ( offset * BIT_PER_CHAR ) );
offset++;
if ( offset == CHAR_PER_WORD )
{
*queryPtr = currentWord;
queryPtr += 32;
offset = 0;
currentWord = 0;
}
}
nucleoId++;
}
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
if ( offset > 0 )
{ *queryPtr = currentWord; }
currentWord = 0;
offset = 0;
readLengths[queriesRead] = nucleoId;
if ( nucleoId == 0 )
{
fprintf ( stderr, "Error! There exists a read with length 0 inside the first read file.\n" );
exit ( EXIT_FAILURE );
}
readIDs[queriesRead] = queriesRead + 1;
if ( nucleoId > maxReadLength )
{
// printf("[WARNING] Left read #%u is longer than %u! Read truncated.\n", (queriesRead+accumReadNum)/2+1, maxReadLength);
readLengths[queriesRead] = maxReadLength;
}
//Parse the quality part of the read
if ( isFastq )
{
//Read everything before the entry point of a read, character "+"
while ( bufferSize != 0 && queryChar != '+' )
{
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
//Read the header of a read
if ( bufferSize == 0 ) { break; }
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
while ( bufferSize != 0 && queryChar != '\n' )
{
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the first file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
//Read the quality of a read
if ( bufferSize == 0 ) { break; }
for ( i = 0; i < nucleoId; i++ )
{
queryChar = queryFileBuffer[bufferIndex++];
if ( queryChar == '\n' )
{ break; }
upkdQualities[queriesRead * maxReadLength + i] = queryChar - qualityConstant;
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
if ( i != nucleoId )
{
fprintf ( stderr, "Error! Inside the first read file, there exists a read of which the number of qualities does not match with the sequence length.\n" );
exit ( EXIT_FAILURE );
}
queryChar = queryFileBuffer[bufferIndex++];
if ( bufferIndex >= bufferSize )
{
bufferSize = gzread ( queryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
}
}
queriesRead += 2;
queryPtr = queries + ( queriesRead / 32 * 32 * wordPerQuery + queriesRead % 32 );
if ( queriesRead >= maxNumQueries )
{ break; }
}
if ( queriesRead == 0 )
{
// no read is loaded
return 0;
}
if ( maxNumQueries > queriesRead )
{ maxNumQueries = queriesRead; }
// FOR THE SECOND READ
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
queriesRead = 1;
queryPtr = queries + ( queriesRead / 32 * 32 * wordPerQuery + queriesRead % 32 );
while ( bufferSize2 != 0 )
{
// FOR THE SECOND READ
//Read everything before the entry point of a read, character ">"
while ( bufferSize2 != 0 && queryChar2 != '>' && queryChar2 != '@' )
{
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
isFastq = 0;
if ( queryChar2 == '@' ) {isFastq = 1;}
//Read the header of a read
if ( bufferSize2 == 0 ) { break; }
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
nameCharId = 0;
cropped = 0;
while ( bufferSize2 != 0 && queryChar2 != '\n' )
{
if ( queryChar2 == ' ' || queryChar2 == '\t' ) {cropped = 1;}
if ( !cropped && nameCharId < maxLenReadName - 1 )
{
upkdQueryNames[queriesRead * maxLenReadName + ( nameCharId++ )] = queryChar2;
}
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
// remove "/1" or "/2" if exists
if ( nameCharId - 2 >= 0 && upkdQueryNames[queriesRead * maxLenReadName + ( nameCharId - 2 )] == '/' )
{ upkdQueryNames[queriesRead * maxLenReadName + ( nameCharId - 2 )] = '\0'; }
else
{ upkdQueryNames[queriesRead * maxLenReadName + nameCharId] = '\0'; }
//Read the pattern body of a read
if ( bufferSize2 == 0 ) { break; }
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
nucleoId = 0;
while ( bufferSize2 != 0 && queryChar2 != '>' && queryChar2 != '@' && queryChar2 != '+' )
{
if ( queryChar2 != '\n' )
{
bits = charMap[queryChar2];
if ( nucleoId < maxReadLength )
{
// upkdQueries[queriesRead*maxReadLength+nucleoId]=bits;
currentWord |= ( bits << ( offset * BIT_PER_CHAR ) );
offset++;
if ( offset == CHAR_PER_WORD )
{
*queryPtr = currentWord;
queryPtr += 32;
offset = 0;
currentWord = 0;
}
}
nucleoId++;
}
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
if ( offset > 0 )
{ *queryPtr = currentWord; }
#ifdef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
// reverse the second read
queryPtr = queries + ( queriesRead / 32 * 32 * wordPerQuery + queriesRead % 32 );
uint readLength = nucleoId;
uint leftWordIndex = 0;
uint rightWordIndex = ( readLength - 1 ) / CHAR_PER_WORD;
uint leftWord = queryPtr[leftWordIndex * 32];
uint rightWord = queryPtr[rightWordIndex * 32];
for ( i = 0, j = readLength - 1; i <= j; ++i, --j )
{
// check if need to move to next word
if ( i / CHAR_PER_WORD != leftWordIndex )
{
// write back leftword
queryPtr[leftWordIndex * 32] = leftWord;
// load next leftword
leftWordIndex++;
leftWord = queryPtr[leftWordIndex * 32];
}
if ( j / CHAR_PER_WORD != rightWordIndex )
{
// write back rightword
queryPtr[rightWordIndex * 32] = rightWord;
// load next rightword
rightWordIndex--;
rightWord = queryPtr[rightWordIndex * 32];
}
// swap left and right characters
unsigned char leftChar = ( leftWord >> ( i % CHAR_PER_WORD * 2 ) ) & CHAR_MASK;
unsigned char rightChar = ( rightWord >> ( j % CHAR_PER_WORD * 2 ) ) & CHAR_MASK;
leftWord ^= ( leftChar ^ ( soap3DnaComplement[rightChar] ) ) << ( i % CHAR_PER_WORD * 2 );
rightWord ^= ( ( soap3DnaComplement[leftChar] ) ^ rightChar ) << ( j % CHAR_PER_WORD * 2 );
}
// write back
if ( leftWordIndex == rightWordIndex )
{
uint numLeftBits = ( ( readLength - 1 ) / 2 % CHAR_PER_WORD + 1 ) * BIT_PER_CHAR;
uint numRightBits = 32 - numLeftBits;
queryPtr[leftWordIndex * 32] = ( ( leftWord << numRightBits ) >> numRightBits ) |
( ( rightWord >> numLeftBits ) << numLeftBits );
}
else
{
queryPtr[leftWordIndex * 32] = leftWord;
queryPtr[rightWordIndex * 32] = rightWord;
}
#endif
currentWord = 0;
offset = 0;
readLengths[queriesRead] = nucleoId;
if ( nucleoId == 0 )
{
fprintf ( stderr, "Error! There exists a read with length 0 inside the second read file.\n" );
exit ( EXIT_FAILURE );
}
readIDs[queriesRead] = queriesRead + 1;
if ( nucleoId > maxReadLength )
{
// printf("[WARNING] Right read #%u is longer than %u! Read truncated.\n", (queriesRead+accumReadNum)/2+1, maxReadLength);
readLengths[queriesRead] = maxReadLength;
}
//Parse the quality part of the read
if ( isFastq )
{
//Read everything before the entry point of a read, character "+"
while ( bufferSize2 != 0 && queryChar2 != '+' )
{
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
//Read the header of a read
if ( bufferSize2 == 0 ) { break; }
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
while ( bufferSize2 != 0 && queryChar2 != '\n' )
{
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
//Read the quality of a read
if ( bufferSize2 == 0 ) { break; }
for ( i = 0; i < nucleoId; i++ )
{
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( queryChar2 == '\n' )
{ break; }
#ifdef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
// reverse the quality of the read
upkdQualities[queriesRead * maxReadLength + nucleoId - 1 - i] = queryChar2 - qualityConstant;
#else
upkdQualities[queriesRead * maxReadLength + i] = queryChar2 - qualityConstant;
#endif
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
if ( i != nucleoId )
{
fprintf ( stderr, "Error! Inside the second read file, there exists a read of which the number of qualities does not match with the sequence length.\n" );
exit ( EXIT_FAILURE );
}
queryChar2 = queryFileBuffer2[bufferIndex2++];
if ( bufferIndex2 >= bufferSize2 )
{
bufferSize2 = gzread ( queryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( queryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( queryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
}
}
queriesRead += 2;
queryPtr = queries + ( queriesRead / 32 * 32 * wordPerQuery + queriesRead % 32 );
if ( queriesRead >= maxNumQueries )
{ break; }
}
queriesRead--; // number of pairs of reads loaded
return queriesRead;
}
// This function is to load the single reads for at most "maxNumQueries" # of reads
int loadSingleReadsGz ( gzFile queryFile, char * queryFileBuffer, unsigned char * charMap,
uint * queries, uint * readLengths, uint * readIDs,
char * upkdQualities, char * upkdQueryNames, uint maxReadLength, uint maxNumQueries,
size_t & bufferSize, char & queryChar, uint & bufferIndex, uint accumReadNum, uint wordPerQuery,
int qualityConstant, char & isFastq, int maxLenReadName )