void
outputObjectFile()
{
void outputPartition();
void outputReferenceInfo();
void outputSymbolTableInfo();
void outputAbsoluteCode();
void outputRelocatableCode();
void outputReservations();
void outputExpressions();
void outputFunctions();
void dumpSymbolTable();
void enumerateAndCountSymbols();
if (debug || emitPrint)
printCodeBuffers();
outputPartition();
outputAbsoluteCode();
if (produceLinkableObject) {
outputPartition();
outputRelocatableCode();
outputPartition();
outputReservations();
outputPartition();
enumerateAndCountSymbols();
outputReferenceInfo();
outputSymbolTableInfo();
outputExpressions();
outputFunctions();
}
if (symbolTableDumpOn)
dumpSymbolTable();
fclose(objectFileOutput);
}
void
partitionBySegment(char *prefix, uint64 numSegments, char *filename) {
seqCache *F = new seqCache(filename);
uint32 n = F->getNumberOfSequences();
partition_s *p = new partition_s [n];
uint32 numSeqPerPart = (uint32)ceil(n / (double)numSegments);
for (uint32 i=0; i<n; i++) {
p[i].length = F->getSequenceLength(i);
p[i].index = i;
p[i].partition = i / numSeqPerPart + 1;
}
outputPartition(F, prefix, p, numSegments, n);
delete [] p;
delete F;
}
void
partitionBySize(char *prefix, uint64 partitionSize, char *filename) {
seqCache *F = new seqCache(filename);
uint32 n = F->getNumberOfSequences();
partition_s *p = loadPartition(F);
uint32 openP = 1; // Currently open partition
uint32 sizeP = 0; // Size of open partition
uint32 seqsP = n; // Number of sequences to partition
// For any sequences larger than partitionSize, create
// partitions containing just one sequence
//
for (uint32 i=0; i<n; i++) {
if (p[i].length > partitionSize) {
p[i].partition = openP++;
seqsP--;
}
}
// For the remaining, iterate through the list,
// greedily placing the longest sequence that fits
// into the open partition
//
while (seqsP > 0) {
for (uint32 i=0; i<n; i++) {
if ((p[i].partition == 0) &&
(p[i].length + sizeP < partitionSize)) {
p[i].partition = openP;
sizeP += p[i].length;
seqsP--;
}
}
openP++;
sizeP = 0;
}
outputPartition(F, prefix, p, openP-1, n);
delete [] p;
delete F;
}
void
partitionByBucket(char *prefix, uint64 partitionSize, char *filename) {
seqCache *F = new seqCache(filename);
uint32 n = F->getNumberOfSequences();
partition_s *p = loadPartition(F);
if (partitionSize > n)
partitionSize = n;
// The size, in bases, of each partition
//
uint32 *s = new uint32 [partitionSize];
for (uint32 i=0; i<partitionSize; i++)
s[i] = 0;
// For each sequence
//
for (uint32 nextS=0; nextS<n; nextS++) {
// find the smallest partition
//
uint32 openP = 0;
for (uint32 i=0; i<partitionSize; i++)
if (s[i] < s[openP])
openP = i;
// add the next largest sequence to the open partition
//
s[openP] += p[nextS].length;
p[nextS].partition = openP+1;
}
outputPartition(F, prefix, p, (uint32)partitionSize, n);
delete [] p;
delete F;
}
