/*
* A thread is trivial if all the segments it contains come from blocks containing only a reference segment.
* These reference only segments represent scaffold gaps. At the same time, it processes the thread string
* to remove the boolean values use to indicate if a thread is trivial or not.
*/
static bool isTrivialString(char **threadString) {
stList *strings = stString_split(*threadString); //Split splits into individual segments.
bool trivialString = 1;
for(int64_t i=0; i<stList_length(strings); i++) {
char *segmentString = stList_get(strings, i);
int64_t j = strlen(segmentString)-1; //Location of the boolean value within a segment.
assert(j > 0);
assert(segmentString[j] == '0' || segmentString[j] == '1');
if(segmentString[j] == '1') { //Found a non-trivial segment, hence the thread is non-trivial.
trivialString = 0;
}
segmentString[j] = '\0';
}
free(*threadString); //Free old thread string. Doing it this way is a bit more memory efficient, as we don't keep two copies of the string around.
*threadString = stString_join2("", strings); //Concatenation makes one sequence, now without the booleans.
stList_destruct(strings);
return trivialString;
}
static void cacheSubstringsFromDB(CactusDisk *cactusDisk, stList *substrings) {
/*
* Caches the given set of substrings in the cactusDisk cache.
*/
if (cactusDisk->storeSequencesInAFile) {
if (cactusDisk->sequencesReadFileHandle == NULL) {
if(cactusDisk->sequencesWriteFileHandle != NULL) {
fsync(fileno(cactusDisk->sequencesWriteFileHandle));
fclose(cactusDisk->sequencesWriteFileHandle);
cactusDisk->sequencesWriteFileHandle = NULL;
}
cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "r");
assert(cactusDisk->sequencesReadFileHandle != NULL);
}
else {
assert(cactusDisk->sequencesWriteFileHandle == NULL);
}
for (int64_t i = 0; i < stList_length(substrings); i++) {
Substring *substring = stList_get(substrings, i);
char *string = getStringFromDisk(cactusDisk->sequencesReadFileHandle, substring->name, substring->start,
substring->length);
stCache_setRecord(cactusDisk->stringCache, substring->name, substring->start, substring->length, string);
#ifndef NDEBUG
int64_t bytesRead;
char *string2 = stCache_getRecord(cactusDisk->stringCache, substring->name, substring->start,
substring->length, &bytesRead);
assert(bytesRead == substring->length);
for (int64_t j = 0; j < substring->length; j++) {
assert(string2[j] == string[j]);
}
free(string2);
#endif
free(string);
}
} else {
stList *getRequests = stList_construct3(0, free);
for (int64_t i = 0; i < stList_length(substrings); i++) {
Substring *substring = stList_get(substrings, i);
int64_t intervalSize = (substring->length + substring->start - 1) / CACTUS_DISK_SEQUENCE_CHUNK_SIZE
- substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1;
Name shiftedName = substring->name + substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE;
for (int64_t j = 0; j < intervalSize; j++) {
int64_t *k = st_malloc(sizeof(int64_t));
k[0] = shiftedName + j;
stList_append(getRequests, k);
}
}
if (stList_length(getRequests) == 0) {
stList_destruct(getRequests);
return;
}
stList *records = NULL;
stTry
{
records = stKVDatabase_bulkGetRecords(cactusDisk->database, getRequests);
}
stCatch(except)
{
stThrowNewCause(except, ST_KV_DATABASE_EXCEPTION_ID,
"An unknown database error occurred when getting a sequence string");
}stTryEnd
;
assert(records != NULL);
assert(stList_length(records) == stList_length(getRequests));
stList_destruct(getRequests);
stListIterator *recordsIt = stList_getIterator(records);
for (int64_t i = 0; i < stList_length(substrings); i++) {
Substring *substring = stList_get(substrings, i);
int64_t intervalSize = (substring->length + substring->start - 1) / CACTUS_DISK_SEQUENCE_CHUNK_SIZE
- substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1;
stList *strings = stList_construct();
while (intervalSize-- > 0) {
int64_t recordSize;
stKVDatabaseBulkResult *result = stList_getNext(recordsIt);
assert(result != NULL);
char *string = stKVDatabaseBulkResult_getRecord(result, &recordSize);
assert(string != NULL);
assert(strlen(string) == recordSize - 1);
stList_append(strings, string);
assert(recordSize <= CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1);
}
assert(stList_length(strings) > 0);
char *joinedString = stString_join2("", strings);
stCache_setRecord(cactusDisk->stringCache, substring->name,
(substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE) * CACTUS_DISK_SEQUENCE_CHUNK_SIZE,
strlen(joinedString), joinedString);
free(joinedString);
stList_destruct(strings);
}
assert(stList_getNext(recordsIt) == NULL);
stList_destructIterator(recordsIt);
stList_destruct(records);
}
}
