bool DynamicBlockBuffer::atomicAppendNewBlock(BlockStreamBase* new_block){
lock_.acquire();
const bool ret=appendNewBlock(new_block);
lock_.release();
return ret;
}
static bool readNextBlock(BinaryFileReaderData * data, char ** lastChrom, int * lastStart, bool * pointByPoint) {
BlockData * block = calloc(1, sizeof(BlockData));
char ** chromPtr = block->chroms;
int * startPtr = block->starts;
int * finishPtr = block->finishes;
double * valuePtr = block->values;
char c;
bool startSet = true;
int32_t holder;
float holder2;
for (block->count = 0; block->count < BLOCK_LENGTH; block->count++) {
// Check whether file finished
if (fread(&c, 1, 1, data->file) == 0) {
appendNewBlock(data, block);
// Increment counter to push the reader into NULL block
pthread_mutex_lock(&data->count_mutex);
data->count++;
pthread_mutex_unlock(&data->count_mutex);
return true;
}
if (*pointByPoint)
startSet = false;
// Read header
if (c == 1) {
// Point by Point
*pointByPoint = true;
mustRead(&c, 1, 1, data->file);
if (c) {
*chromPtr = calloc(1000, 1);
char * ptr = * chromPtr;
int pos;
for (pos = 0; pos < 1000 && c; pos++) {
*ptr = c;
mustRead(&c, 1, 1, data->file);
ptr++;
}
while (c)
mustRead(&c, 1, 1, data->file);
}
mustRead(&holder, sizeof(int32_t), 1, data->file);
*startPtr = holder;
startSet = true;
} else if (c == 2) {
// Normal
*pointByPoint = false;
mustRead(&c, 1, 1, data->file);
if (c) {
*chromPtr = calloc(1000, 1);
char * ptr = * chromPtr;
int pos;
for (pos = 0; pos < 1000 && c; pos++) {
*ptr = c;
mustRead(&c, 1, 1, data->file);
ptr++;
}
while (c)
mustRead(&c, 1, 1, data->file);
}
}
// Set chromosome if unset in header
if (*chromPtr == NULL)
*chromPtr = *lastChrom;
// Read coords
if (*pointByPoint) {
if (!startSet)
*startPtr = *lastStart + 1;
*finishPtr = *startPtr + 1;
} else {
mustRead(&holder, sizeof(int32_t), 1, data->file);
*startPtr = holder;
mustRead(&holder, sizeof(int32_t), 1, data->file);
*finishPtr = holder;
}
// Read value
mustRead(&holder2, sizeof(float), 1, data->file);
*valuePtr = holder2;
// Record stuff
*lastChrom = *chromPtr;
*lastStart = *startPtr;
// Step ahead
chromPtr++;
startPtr++;
finishPtr++;
valuePtr++;
}
return appendNewBlock(data, block);
}