void
writeUnitigsToStore(UnitigVector &unitigs,
char *fileprefix,
char *tigStorePath,
uint32 frg_count_target,
bool isFinal) {
uint32 utg_count = 0;
uint32 frg_count = 0;
uint32 prt_count = 1;
char filename[FILENAME_MAX] = {0};
uint32 *partmap = new uint32 [unitigs.size()];
// This code closely follows that in AS_CGB_unitigger.c::output_the_chunks()
if (isFinal)
checkUnitigMembership(unitigs);
// Open up the initial output file
sprintf(filename, "%s.iidmap", fileprefix);
FILE *iidm = fopen(filename, "w");
assert(NULL != iidm);
sprintf(filename, "%s.partitioning", fileprefix);
FILE *part = fopen(filename, "w");
assert(NULL != part);
sprintf(filename, "%s.partitioningInfo", fileprefix);
FILE *pari = fopen(filename, "w");
assert(NULL != pari);
// Step through all the unitigs once to build the partition mapping and IID mapping.
memset(partmap, 0xff, sizeof(uint32) * unitigs.size());
for (uint32 iumiid=0, ti=0; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
uint32 nf = (utg) ? utg->getNumFrags() : 0;
if ((utg == NULL) || (nf == 0))
continue;
assert(utg->getLength() > 0);
assert(nf == utg->ufpath.size());
if ((frg_count + nf >= frg_count_target) &&
(frg_count > 0)) {
fprintf(pari, "Partition %d has %d unitigs and %d fragments.\n",
prt_count, utg_count, frg_count);
prt_count++;
utg_count = 0;
frg_count = 0;
}
uint32 tigid = (isFinal) ? iumiid : ti;
assert(tigid < unitigs.size());
partmap[tigid] = prt_count;
fprintf(iidm, "Unitig "F_U32" == IUM "F_U32" (in partition "F_U32" with "F_U32" frags)\n",
utg->id(),
(tigid),
partmap[(tigid)],
nf);
for (uint32 fragIdx=0; fragIdx<nf; fragIdx++) {
ufNode *f = &utg->ufpath[fragIdx];
fprintf(part, "%d\t%d\n", prt_count, f->ident);
}
utg_count += 1;
frg_count += nf;
iumiid++;
}
fprintf(pari, "Partition %d has %d unitigs and %d fragments.\n",
prt_count, utg_count, frg_count);
fclose(pari);
fclose(part);
fclose(iidm);
// Step through all the unitigs once to build the partition mapping and IID mapping.
tgStore *tigStore = new tgStore(tigStorePath);
tgTig *tig = new tgTig;
for (uint32 iumiid=0, ti=0; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
uint32 nf = (utg) ? utg->getNumFrags() : 0;
if ((utg == NULL) || (nf == 0))
continue;
unitigToTig(tig, (isFinal) ? iumiid : ti, utg);
tigStore->insertTig(tig, false);
iumiid++;
}
delete tig;
delete tigStore;
delete [] partmap;
}
void
writeUnitigsToStore(UnitigVector &unitigs,
char *fileprefix,
char *tigStorePath,
uint32 frg_count_target,
bool isFinal) {
uint32 utg_count = 0;
uint32 frg_count = 0;
uint32 prt_count = 1;
char filename[FILENAME_MAX] = {0};
uint32 *partmap = new uint32 [unitigs.size()];
// This code closely follows that in AS_CGB_unitigger.c::output_the_chunks()
if (isFinal)
checkUnitigMembership(unitigs);
// Open up the initial output file
sprintf(filename, "%s.iidmap", fileprefix);
FILE *iidm = fopen(filename, "w");
assert(NULL != iidm);
sprintf(filename, "%s.partitioning", fileprefix);
FILE *part = fopen(filename, "w");
assert(NULL != part);
sprintf(filename, "%s.partitioningInfo", fileprefix);
FILE *pari = fopen(filename, "w");
assert(NULL != pari);
// Step through all the unitigs once to build the partition mapping and IID mapping.
tgStore *tigStore = new tgStore(tigStorePath);
tgTig *tig = new tgTig;
for (uint32 tigID=0, ti=0; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
if ((utg == NULL) || (utg->getNumFrags() == 0))
continue;
assert(utg->getLength() > 0);
// Convert the bogart tig to a tgTig and save to the store.
unitigToTig(tig, (isFinal) ? tigID : ti, utg);
tigID++;
tigStore->insertTig(tig, false);
// Increment the partition if the current one is too large.
if ((frg_count + utg->getNumFrags() >= frg_count_target) &&
(frg_count > 0)) {
fprintf(pari, "Partition %d has %d unitigs and %d fragments.\n",
prt_count, utg_count, frg_count);
prt_count++;
utg_count = 0;
frg_count = 0;
}
// Note that the tig is included in this partition.
utg_count += 1;
frg_count += utg->getNumFrags();
// Map the tig to a partition, and log both the tig-to-partition map and the partition-to-read map.
fprintf(iidm, "bogart "F_U32" -> tig "F_U32" (in partition "F_U32" with "F_U32" frags)\n",
utg->id(),
utg->tigID(),
prt_count,
utg->getNumFrags());
for (uint32 fragIdx=0; fragIdx<utg->getNumFrags(); fragIdx++)
fprintf(part, "%d\t%d\n", prt_count, utg->ufpath[fragIdx].ident);
}
fprintf(pari, "Partition %d has %d unitigs and %d fragments.\n", // Don't forget to log the last partition!
prt_count, utg_count, frg_count);
fclose(pari);
fclose(part);
fclose(iidm);
delete tig;
delete tigStore;
}
