// Free memory used to store unpacked regions
void unpack_free() {
struct unpackRegion *region;
// For each unpack region
if (!parameters_ssearch && encoding_alphabetType == encoding_nucleotide) {
memBlocks_resetCurrent(unpack_unpackRegions);
while ((region = memBlocks_getCurrent(unpack_unpackRegions)) != NULL) {
// Free the unpacked sequence
free(region->unpackedSubject + region->startOffset);
}
}
// For each copied subject region
memBlocks_resetCurrent(unpack_subjectRegions);
while ((region = memBlocks_getCurrent(unpack_subjectRegions)) != NULL) {
// Free the subject
free(region->subject + region->startOffset / 4);
}
memBlocks_free(unpack_unpackRegions);
memBlocks_free(unpack_subjectRegions);
}
// Given a query sequence uses an inverted index of the collection to identify the
// sequence number and offset of all hits between the query and the collection
void index_processQuery(unsigned char* startIndex, struct PSSMatrix PSSMatrix,
uint4 numSequences)
{
uint4 queryPosition, codeword = 0, queryPosition4;
unsigned char* offsets, *endOffsets;
uint4 offsetGap, offset, sequenceGap, sequenceNumber;
struct indexCoordinate* coordinate;
struct memBlocks* unsortedCoordinates;
uint4 *numSubjectHits, numQueryPositions, queryWordCount, numOffsets;
uint4 time, wordPosition, containsWildcard;
struct queryWord* queryWords;
// Read word and interval size from start of index
vbyte_getVbyte(startIndex, &index_wordSize);
vbyte_getVbyte(startIndex, &index_intervalSize);
index_numWords = pow(4, index_wordSize);
index_sequencePositions = (uint4*)startIndex;
index_descriptionLocations = index_sequencePositions + numSequences;
index_loadedWords = index_descriptionLocations + numSequences;
index_offsets = (unsigned char*)(index_loadedWords + index_numWords + 1);
time = clock();
unsortedCoordinates = memBlocks_initialize(sizeof(struct indexCoordinate), numSequences);
// Declare and initialize array for count number of hits for each sequence
numSubjectHits = (uint*)global_malloc(sizeof(uint4) * numSequences);
sequenceNumber = 0;
while (sequenceNumber < numSequences)
{
numSubjectHits[sequenceNumber] = 0;
sequenceNumber++;
}
// Memory to hold offsets string for each query word
numQueryPositions = PSSMatrix.length - index_wordSize + 1;
queryWords = (struct queryWord*)global_malloc(sizeof(struct queryWord) * numQueryPositions);
// For each word in the query
queryPosition = 0;
while (queryPosition < numQueryPositions)
{
// Check if the word contains a wildcard
containsWildcard = 0; wordPosition = 0;
while (wordPosition < index_wordSize)
{
if (PSSMatrix.queryCodes[queryPosition + wordPosition] >= encoding_numRegularLetters)
containsWildcard = 1;
wordPosition++;
}
// Don't include words that cross the strand boundry or contain wildcards
if (!containsWildcard && !(queryPosition < PSSMatrix.strandLength &&
queryPosition >= PSSMatrix.strandLength - index_wordSize + 1))
{
// printf("--Query position=%d\n", queryPosition);
// Get the codeword
codeword = index_generateCodeword(PSSMatrix.bestMatchCodes + queryPosition, index_wordSize);
// Get wordlist for that codeword
offsets = index_offsets + index_loadedWords[codeword];
endOffsets = index_offsets + index_loadedWords[codeword + 1];
queryWords[queryPosition].offsets = offsets;
queryWords[queryPosition].endOffsets = endOffsets;
queryWords[queryPosition].queryPosition = queryPosition;
queryWords[queryPosition].codeword = codeword;
// printf("codeword=%d start=%d end=%d numHits=%d\n", codeword, index_loadedWords[codeword],
// index_loadedWords[codeword + 1], endOffsets - offsets);
}
else
{
queryWords[queryPosition].offsets = NULL;
queryWords[queryPosition].endOffsets = NULL;
queryWords[queryPosition].queryPosition = queryPosition;
queryWords[queryPosition].codeword = codeword;
}
// printf("\n");
queryPosition++;
}
// Sort the query words by codeword
qsort(queryWords, numQueryPositions, sizeof(struct queryWord), alignments_compareCodeword);
// For each query word
queryWordCount = 0;
while (queryWordCount < numQueryPositions)
{
// Ignoring those that cross the strand boundry
if (queryWords[queryWordCount].offsets != NULL)
{
// Make in-memory copy of list of offsets
numOffsets = queryWords[queryWordCount].endOffsets - queryWords[queryWordCount].offsets;
offsets = (char*)global_malloc(sizeof(char) * numOffsets);
memcpy(offsets, queryWords[queryWordCount].offsets, numOffsets);
queryWords[queryWordCount].offsets = offsets;
queryWords[queryWordCount].endOffsets = offsets + numOffsets;
}
queryWordCount++;
}
// Sort the query words by query position
qsort(queryWords, numQueryPositions, sizeof(struct queryWord), alignments_compareQueryPosition);
queryPosition = 0;
while (queryPosition < numQueryPositions)
{
// Ignoring those that cross the strand boundry
if (queryWords[queryPosition].offsets != NULL)
{
offsets = queryWords[queryPosition].offsets;
endOffsets = queryWords[queryPosition].endOffsets;
offset = 0;
sequenceNumber = 0;
queryPosition4 = queryPosition + (index_wordSize - 4);
// Traverse the offsets
while (offsets < endOffsets)
{
vbyte_getVbyte(offsets, (&sequenceGap));
vbyte_getVbyte(offsets, (&offsetGap));
// printf("[%d,%d]\n", sequenceGap, offsetGap);
if (sequenceGap > 0)
{
offset = offsetGap;
sequenceNumber += sequenceGap;
}
else
{
offset += offsetGap;
}
// printf(" %u", offset);
// Add query/database coordinate of match to relevant bucket
// printf("Sequence number=%d\n", sequenceNumber);
coordinate = (struct indexCoordinate*)memBlocks_newEntry(unsortedCoordinates);
coordinate->queryOffset = queryPosition4;
coordinate->subjectOffset = offset * index_intervalSize + (index_wordSize - 4);
coordinate->subjectNumber = sequenceNumber;
numSubjectHits[sequenceNumber]++;
// printf("[%d,%d]\n", queryPosition, offset);
blast_numHits++;
}
free(queryWords[queryPosition].offsets);
}
queryPosition++;
}
printf("Time to process query=%f\n", (float)(clock() - time) / CLOCKS_PER_SEC);
time = clock();
// Make memory for sorted list
index_numCoordinates = unsortedCoordinates->numTotalEntries;
index_coordinates = (struct indexCoordinate*)global_malloc(
sizeof(struct indexCoordinate) * index_numCoordinates);
index_sequenceCoordinates = (struct indexCoordinate**)global_malloc(
sizeof(struct indexCoordinate*) * numSequences);
// For each sequence
coordinate = index_coordinates;
sequenceNumber = 0;
while (sequenceNumber < numSequences)
{
// If it has hits
if (numSubjectHits[sequenceNumber] != 0)
{
// Point to location in sorted list of coordinates
index_sequenceCoordinates[sequenceNumber] = coordinate;
coordinate += numSubjectHits[sequenceNumber];
numSubjectHits[sequenceNumber] = 0;
}
sequenceNumber++;
}
// Move through list of unsorted coordinates
memBlocks_resetCurrent(unsortedCoordinates);
while ((coordinate = memBlocks_getCurrent(unsortedCoordinates)) != NULL)
{
sequenceNumber = coordinate->subjectNumber;
// printf("%d,%d=[%d]\n", index_sequenceCoordinates[sequenceNumber], numSubjectHits[sequenceNumber], sequenceNumber);
// Place into sorted list
index_sequenceCoordinates[sequenceNumber][numSubjectHits[sequenceNumber]] = *coordinate;
numSubjectHits[sequenceNumber]++;
}
memBlocks_free(unsortedCoordinates);
/* // Print sorted coordinates
coordinate = index_coordinates;
while (coordinate < index_coordinates + index_numCoordinates)
{
printf("[%d]", coordinate);
printf("Subject %d Offset %d,%d\n", coordinate->subjectNumber, coordinate->queryOffset,
coordinate->subjectOffset);
coordinate++;
}*/
printf("Time to sort buckets=%f\n", (float)(clock() - time) / CLOCKS_PER_SEC);
}
// Finalize writing to the formatted collection
void writedb_close() {
unsigned char headerData[100], *headerDataPointer;
uint4 headerLength;
struct sequenceData *sequenceData;
// Write sentinal/padding byte at end
if (writedb_alphabetType == encoding_protein)
fputc(encoding_sentinalCode, writedb_sequenceFile);
else
fputc(0, writedb_sequenceFile);
// Close writing to sequence and description files
fclose(writedb_sequenceFile);
fclose(writedb_descriptionsFile);
// Open data file for writing
if ((writedb_dataFile = fopen(writedb_dataFilename, "w")) == NULL) {
fprintf(stderr, "Error opening file %s for writing\n",
writedb_dataFilename);
exit(-1);
}
// Convert 6 header values to vbytes
headerDataPointer = headerData;
vbyte_safePutVbyte(headerDataPointer, constants_databaseVersion);
vbyte_safePutVbyte(headerDataPointer, writedb_sequenceCount);
vbyte_safePutVbyte(headerDataPointer, writedb_numberOfLetters);
vbyte_safePutVbyte(headerDataPointer, writedb_maximumSequenceLength);
vbyte_safePutVbyte(headerDataPointer, writedb_alphabetType);
vbyte_safePutVbyte(headerDataPointer, writedb_numberOfClusters);
vbyte_safePutVbyte(headerDataPointer, writedb_volume + 1);
// Write the header data at the start of the file
headerLength = headerDataPointer - headerData;
if (fwrite(&headerData, sizeof(unsigned char), headerLength,
writedb_dataFile) < headerLength) {
fprintf(stderr, "Error writing header to sequence file %s\n",
writedb_dataFilename);
exit(-1);
}
// For each sequence
memBlocks_resetCurrent(writedb_sequenceData);
while ((sequenceData = memBlocks_getCurrent(writedb_sequenceData)) != NULL) {
// Prepare to write sequence description length, subject length, and encoded
// length using vbytes
headerDataPointer = headerData;
vbyte_safePutVbyte(headerDataPointer, sequenceData->descriptionLength);
vbyte_safePutVbyte(headerDataPointer, sequenceData->sequenceLength);
vbyte_safePutVbyte(headerDataPointer, sequenceData->encodedLength);
vbyte_safePutVbyte(headerDataPointer, sequenceData->oid);
// Write sequence header information
headerLength = headerDataPointer - headerData;
if (fwrite(headerData, sizeof(unsigned char), headerLength,
writedb_dataFile) < headerLength) {
fprintf(stderr, "Error writing to sequence file %s\n",
writedb_dataFilename);
exit(-1);
}
}
// Close writing to sequence file
fclose(writedb_dataFile);
memBlocks_free(writedb_sequenceData);
}
