rc_t CC FastqReaderFileMake( const ReaderFile **reader,
const KDirectory* dir,
const char* file,
enum FASTQQualityFormat qualityFormat,
int8_t defaultReadNumber,
bool ignoreSpotGroups)
{
rc_t rc;
FastqReaderFile* self = (FastqReaderFile*) malloc ( sizeof * self );
if ( self == NULL )
{
rc = RC ( RC_MODULE, rcFileFormat, rcAllocating, rcMemory, rcExhausted );
}
else
{
memset(self, 0, sizeof(*self));
rc = ReaderFileInit ( self );
self->dad.vt.v1 = & FastqReaderFile_vt;
self->dad.pathname = string_dup(file, strlen(file)+1);
if ( self->dad.pathname == NULL )
{
rc = RC ( RC_MODULE, rcFileFormat, rcAllocating, rcMemory, rcExhausted );
}
else
{
rc = KLoaderFile_Make( & self->reader, dir, file, 0, true );
}
if (rc == 0)
{
self->pb.self = self;
self->pb.input = FASTQ_input;
self->pb.qualityFormat = qualityFormat;
self->pb.defaultReadNumber = defaultReadNumber;
self->pb.secondaryReadNumber = 0;
self->pb.ignoreSpotGroups = ignoreSpotGroups;
rc = FASTQScan_yylex_init(& self->pb, false);
if (rc == 0)
{
*reader = (const ReaderFile *) self;
}
else
{
KLoaderFile_Release( self->reader, true );
ReaderFileRelease( & self->dad );
*reader = 0;
}
}
else
{
ReaderFileRelease( & self->dad );
*reader = 0;
}
}
return rc;
}
rc_t FastqReaderFileWhack( FastqReaderFile* f )
{
FastqReaderFile* self = (FastqReaderFile*) f;
FASTQScan_yylex_destroy(& self->pb);
if (self->reader)
KLoaderFile_Release ( self->reader, true );
ReaderFileWhack( &self->dad );
free ( self );
return 0;
}
LIB_EXPORT rc_t CC KLoaderFile_Make(const KLoaderFile **file, const KDirectory* dir, const char* filename,
const uint8_t* md5_digest, bool read_ahead)
{
rc_t rc = 0;
KLoaderFile* obj = NULL;
if( file == NULL || dir == NULL || filename == NULL ) {
rc = RC(rcApp, rcFile, rcConstructing, rcParam, rcNull);
} else {
*file = NULL;
if( (obj = calloc(1, sizeof(*obj))) == NULL ||
(obj->filename = strdup(filename)) == NULL ) {
rc = RC(rcApp, rcFile, rcConstructing, rcMemory, rcExhausted);
} else {
if( (rc = KDirectoryAddRef(dir)) == 0 ) {
obj->dir = dir;
if( md5_digest != NULL ) {
obj->has_md5 = true;
memcpy(obj->md5_digest, md5_digest, sizeof(obj->md5_digest));
}
if( (rc = KLoaderFile_AllocateBuffer(obj)) == 0 ) {
char resolved[4096];
char* ext = NULL;
strcpy(resolved, filename);
ext = strrchr(resolved, '.');
DBG(("%s adding %s\n", __func__, resolved));
rc = KLoadProgressbar_File(&obj->job, resolved, obj->dir);
if( ext != NULL && strcmp(ext, ".gz") == 0 ) {
obj->compress_type = compress_gzip;
} else if( ext != NULL && strcmp(ext, ".bz2") == 0 ) {
obj->compress_type = compress_bzip2;
}
if( rc != 0 && obj->compress_type != compress_none ) {
*ext = '\0';
DBG(("%s retry adding as %s\n", __func__, resolved));
if( (rc = KLoadProgressbar_File(&obj->job, resolved, obj->dir)) == 0 ) {
obj->has_md5 = false;
obj->compress_type = compress_none;
}
}
if( rc == 0 &&
(rc = KFileInit(&obj->dad, (const KFile_vt*)&KLoaderFile_vtbl, "KLoaderFile", filename, true, false)) == 0 ) {
obj->file = &obj->dad;
#if WINDOWS
obj->ahead = false;
#else
obj->ahead = read_ahead;
#endif
obj->realname = strdup(resolved);
if( obj->realname == NULL ) {
rc = RC(rcApp, rcFile, rcConstructing, rcMemory, rcExhausted);
}
}
}
}
}
}
if( rc == 0 ) {
*file = obj;
} else {
*file = NULL;
KLoaderFile_Release(obj, false);
}
return rc;
}
