// For every unitig, report the best overlaps contained in the
// unitig, and all overlaps contained in the unitig.
//
// Wow, this is ancient.
//
void
writeOverlapsUsed(UnitigVector &unitigs,
char *prefix) {
char N[FILENAME_MAX];
sprintf(N, "%s.unused.best.edges", prefix);
FILE *F = fopen(N, "w");
for (uint32 ti=0; ti<unitigs.size(); ti++) {
Unitig *tig = unitigs[ti];
Unitig *ovl = NULL;
char tyt = 'C';
if (tig == NULL)
continue;
if (tig->_isUnassembled) tyt = 'U';
if (tig->_isBubble) tyt = 'B';
if (tig->_isRepeat) tyt = 'R';
if (tig->_isCircular) tyt = 'O';
for (uint32 fi=0; fi<tig->ufpath.size(); fi++) {
ufNode *frg = &tig->ufpath[fi];
ufNode *oth = NULL;
// Report the unused best edge
BestEdgeOverlap *be5 = OG->getBestEdgeOverlap(frg->ident, false);
uint32 rd5 = (be5 == NULL) ? 0 : be5->fragId();
Unitig *tg5 = (be5 == NULL) ? NULL : unitigs[Unitig::fragIn(rd5)];
char ty5 = 'C';
if ((tg5 != NULL) && (tg5->tigID() != tig->tigID())) {
uint32 ord = Unitig::pathPosition(rd5);
ufNode *oth = &tg5->ufpath[ord];
if (tig->_isUnassembled) ty5 = 'U';
if (tig->_isBubble) ty5 = 'B';
if (tig->_isRepeat) ty5 = 'R';
if (tig->_isCircular) ty5 = 'O';
fprintf(F, "tig %7u %c read %8u at %9u %-9u %c' -- %8d %-8d -- tig %7u %c read %8u at %9u %-9u %c'\n",
tig->tigID(), tyt, frg->ident, frg->position.bgn, frg->position.end, '5',
be5->ahang(), be5->bhang(),
tg5->tigID(), ty5, oth->ident, oth->position.bgn, oth->position.end, (be5->frag3p() == false) ? '5' : '3');
}
BestEdgeOverlap *be3 = OG->getBestEdgeOverlap(frg->ident, true);
uint32 rd3 = (be3 == NULL) ? 0 : be3->fragId();
Unitig *tg3 = (be3 == NULL) ? NULL : unitigs[Unitig::fragIn(rd3)];
char ty3 = 'C';
if ((tg3 != NULL) && (tg3->tigID() != tig->tigID())) {
uint32 ord = Unitig::pathPosition(rd3);
ufNode *oth = &tg3->ufpath[ord];
if (tig->_isUnassembled) ty3 = 'U';
if (tig->_isBubble) ty3 = 'B';
if (tig->_isRepeat) ty3 = 'R';
if (tig->_isCircular) ty3 = 'O';
fprintf(F, "tig %7u %c read %8u at %9u %-9u %c' -- %8d %-8d -- tig %7u %c read %8u at %9u %-9u %c'\n",
tig->tigID(), tyt, frg->ident, frg->position.bgn, frg->position.end, '3',
be3->ahang(), be3->bhang(),
tg3->tigID(), ty3, oth->ident, oth->position.bgn, oth->position.end, (be3->frag3p() == false) ? '5' : '3');
}
}
}
fclose(F);
}
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;
}
