// Open a file. Called by the constructor.
// Returns true if the file was successfully opened, false otherwise.
bool InputFile::openFile(const char * filename, const char * mode,
InputFile::ifileCompression compressionMode)
{
// If a file is for write, just open a new file.
if (mode[0] == 'w' || mode[0] == 'W')
{
openFileUsingMode(filename, mode, compressionMode);
}
else
{
// Check if reading from stdin.
if(strcmp(filename, "-") == 0)
{
// Reading from stdin, open it based on the
// compression mode.
openFileUsingMode(filename, mode, compressionMode);
}
else
{
// Not from stdin, so determine the file type.
// Open the file read only to determine file type.
FILE* filePtr = fopen(filename, "r");
// If the file could not be opened, either create a new one or
// return failure.
if (filePtr == NULL)
{
// If the mode is for read, then the file must exist, otherwise,
// create a new file.
if (mode[0] == 'r' || mode[0] == 'R')
{
// File must exist.
if (myFileTypePtr != NULL)
{
delete myFileTypePtr;
myFileTypePtr = NULL;
}
// Return false, was not opened.
return false;
}
else
{
openFileUsingMode(filename, mode, compressionMode);
}
}
else
{
// File was successfully opened, so try to determine the
// filetype from the file.
// Read the file to see if it a gzip file.
GzipHeader gzipHeader;
bool isGzip = gzipHeader.readHeader(filePtr);
// The file header has been read, so close the file, so it can
// be re-opened as the correct type.
fclose(filePtr);
if (isGzip)
{
// This file is a gzip file.
// Check to see if it is BGZF Compression.
if (gzipHeader.isBgzfFile())
{
// This file has BGZF Compression, so set the file
// pointer.
myFileTypePtr = new BgzfFileType(filename, mode);
}
else
{
// Not BGZF, just a normal gzip.
myFileTypePtr = new GzipFileType(filename, mode);
}
}
else
{
// The file is a uncompressed, uncompressed file,
// so set the myFileTypePtr accordingly.
myFileTypePtr = new UncompressedFileType(filename, mode);
}
}
}
}
if(myFileTypePtr == NULL)
{
return(false);
}
if (!myFileTypePtr->isOpen())
{
// The file was not opened, so delete the pointer and set to null.
delete myFileTypePtr;
myFileTypePtr = NULL;
return false;
}
if(myAllocatedBufferSize == 1)
{
myFileTypePtr->setBuffered(false);
}
else
{
myFileTypePtr->setBuffered(true);
}
myFileName = filename;
return true;
}
// Open a file. Called by the constructor.
// Returns true if the file was successfully opened, false otherwise.
bool InputFile::openFile(const char * filename, const char * mode,
InputFile::ifileCompression compressionMode)
{
//
// if recovering, we don't want to issue big readaheads, since
// that interferes with the decompression - we only want to
// decompress one at a time, and handle the exceptions immediately
// rather than at some indeterminate point in time.
//
if(myAttemptRecovery) {
bufferReads(1);
}
// If a file is for write, just open a new file.
if (mode[0] == 'w' || mode[0] == 'W')
{
openFileUsingMode(filename, mode, compressionMode);
}
else
{
// Check if reading from stdin.
if((strcmp(filename, "-") == 0) || (strcmp(filename, "-.gz") == 0))
{
// Reading from stdin, open it based on the
// compression mode.
openFileUsingMode(filename, mode, compressionMode);
}
else
{
// Not from stdin, so determine the file type.
// Open the file read only to determine file type.
FILE* filePtr = fopen(filename, "r");
// If the file could not be opened, either create a new one or
// return failure.
if (filePtr == NULL)
{
// If the mode is for read, then the file must exist, otherwise,
// create a new file.
if (mode[0] == 'r' || mode[0] == 'R')
{
// File must exist.
if (myFileTypePtr != NULL)
{
delete myFileTypePtr;
myFileTypePtr = NULL;
}
// Return false, was not opened.
return false;
}
else
{
openFileUsingMode(filename, mode, compressionMode);
}
}
else
{
// File was successfully opened, so try to determine the
// filetype from the file.
// Read the file to see if it a gzip file.
GzipHeader gzipHeader;
bool isGzip = gzipHeader.readHeader(filePtr);
// The file header has been read, so close the file, so it can
// be re-opened as the correct type.
fclose(filePtr);
if (isGzip)
{
// This file is a gzip file.
// Check to see if it is BGZF Compression.
if (gzipHeader.isBgzfFile())
{
// This file has BGZF Compression, so set the file
// pointer.
if(myAttemptRecovery) {
// NB: this reader will throw std::runtime_error when it recovers
myFileTypePtr = new BgzfFileTypeRecovery(filename, mode);
} else {
// use the standard bgzf reader (samtools)
myFileTypePtr = new BgzfFileType(filename, mode);
}
}
else
{
// Not BGZF, just a normal gzip.
myFileTypePtr = new GzipFileType(filename, mode);
}
}
else
{
// The file is a uncompressed, uncompressed file,
// so set the myFileTypePtr accordingly.
myFileTypePtr = new UncompressedFileType(filename, mode);
}
}
}
}
if(myFileTypePtr == NULL)
{
return(false);
}
if (!myFileTypePtr->isOpen())
{
// The file was not opened, so delete the pointer and set to null.
delete myFileTypePtr;
myFileTypePtr = NULL;
return false;
}
if(myAllocatedBufferSize == 1)
{
myFileTypePtr->setBuffered(false);
}
else
{
myFileTypePtr->setBuffered(true);
}
myFileName = filename;
return true;
}
