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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
* Copyright (C) 2013 Sébastien Boisvert
*
* http://DeNovoAssembler.SourceForge.Net/
*
* 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, version 3 of the License.
*
* 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 have received a copy of the GNU General Public License
* along with this program (gpl-3.0.txt).
* see <http://www.gnu.org/licenses/>
*/
#include "BufferedReader.h"
#include <code/Mock/constants.h>
#include <iostream>
using namespace std;
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#ifdef CONFIG_ASSERT
#include <assert.h>
#endif
//#define CONFIG_FASTQ_DEBUG_MESSAGE
#define CONFIG_FASTQ_BUFFER_SIZE SIZE_4M
void BufferedReader::initialize() {
m_assetCacheMaximumLength = CONFIG_FASTQ_BUFFER_SIZE;
m_assetCacheContent = (char*) malloc(m_assetCacheMaximumLength * sizeof(char));
reset();
}
void BufferedReader::reset() {
m_assetCacheLength = 0;
m_assetCacheOffset = 0;
}
/**
* This is a drop-in replacement for fgets with buffering features.
*
* \see http://www.cplusplus.com/reference/cstdio/fgets/
* \see http://www.cplusplus.com/reference/cstdio/feof/
* \see http://www.cplusplus.com/reference/cstdio/fread/
*
* TODO This method will not work properly if numberOfBytes is > CONFIG_FASTQ_BUFFER_SIZE
* TODO Also, it will not work if lines from the content stream are longer than CONFIG_FASTQ_BUFFER_SIZE.
*
* \author Sébastien Boisvert
* \see https://github.com/sebhtml/ray/issues/137
*
*
* m_assetCacheContent -> the content
* m_assetCacheLength -> the size of the content
* m_assetCacheOffset -> the current offset in the content
* m_assetCacheMaximumLength -> the maximum size
*/
char * BufferedReader::readLine(char * content, int numberOfBytes, FILE * endpoint){
//cout << "[DEBUG] readLine" << endl;
//return fgets(content, numberOfBytes, endpoint);
return readLineFromBuffer(content, numberOfBytes, endpoint, true);
}
/**
*
*/
char * BufferedReader::readLineFromBuffer(char * content, int numberOfBytes, FILE * endpoint, bool retry) {
if(copyWithNewLine(content))
return content;
if(retry) {
fillBuffer(endpoint);
return readLineFromBuffer(content, numberOfBytes, endpoint, false);
}
if(copyWithMaximumNumberOfBytes(content, numberOfBytes))
return content;
return NULL;
}
void BufferedReader::fillBuffer(FILE * source) {
//cout << "[DEBUG] fillBuffer " << endl;
moveBuffer();
char * buffer = getBuffer();
int bufferSize = getBufferSize();
int maximumBufferSize = getMaximumBufferSize();
int available = maximumBufferSize - bufferSize;
char * destination = buffer + bufferSize;
int elements = fread(destination, sizeof(char), available, source);
m_assetCacheLength += elements;
}
int BufferedReader::getMaximumBufferSize() {
return m_assetCacheMaximumLength;
}
void BufferedReader::moveBuffer() {
int source = m_assetCacheOffset;
int destination = 0;
while(source < m_assetCacheLength) {
m_assetCacheContent[destination] = m_assetCacheContent[source];
destination++;
source++;
}
m_assetCacheLength -= m_assetCacheOffset;
m_assetCacheOffset = 0;
}
char * BufferedReader::getBuffer() {
return m_assetCacheContent + m_assetCacheOffset;
}
int BufferedReader::getBufferSize() {
return m_assetCacheLength - m_assetCacheOffset;
}
int BufferedReader::findNewLine(char * sequence, int length) {
int i = 0;
while(i < length) {
if(sequence[i] == '\n')
return i;
i++;
}
return -1;
}
bool BufferedReader::copyWithNewLine(char * content) {
char * buffer = getBuffer();
int bufferSize = getBufferSize();
int newLinePosition = findNewLine(buffer, bufferSize);
if(newLinePosition < 0)
return false;
int count = newLinePosition + 1;
consumeContent(buffer, content, count);
return true;
}
bool BufferedReader::copyWithMaximumNumberOfBytes(char * content, int numberOfBytes) {
int availableBytes = getBufferSize();
if(availableBytes == 0)
return false;
char * buffer = getBuffer();
int count = numberOfBytes;
if(availableBytes < count)
count = availableBytes;
consumeContent(buffer, content, count);
return true;
}
void BufferedReader::consumeContent(char * buffer, char * content, int count) {
memcpy(content, buffer, count);
content[count] = '\0';
m_assetCacheOffset += count;
}
void BufferedReader::destroy() {
if(m_assetCacheContent != NULL) {
free(m_assetCacheContent);
}
m_assetCacheContent = NULL;
m_assetCacheLength = 0;
m_assetCacheMaximumLength = 0;
}
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