bool Alignment::init(const LcbList & lcbList, const VariantList & variantList, const ReferenceList & referenceList, const TrackList & trackList)
{
totalLength = 0;
filterFlags = 0;
filterPass = true;
filterPassScale = true;
filterShow = false;
trackReference = 0;
destroyRegions();
lcbs.resize(lcbList.getLcbCount());
tracks.resize(trackList.getTrackCount());
for ( int i = 0; i < tracks.size(); i++ )
{
tracks[i] = new QVector<Region *>(lcbList.getLcbCount());
}
for ( int i = 0; i < lcbList.getLcbCount(); i++ )
{
const LcbList::Lcb & lcb = lcbList.getLcb(i);
int id = i;
lcbs[id].concordance = 1 - lcb.concordance;
//lcbs[id].number = atoi(lcb.name().c_str());
QVector<Region *> * regions = new QVector<Region *>(lcb.regions.size());
for ( int j = 0; j < lcb.regions.size(); j++ )
{
const LcbList::Region & lcbRegion = lcb.regions.at(j);
int track = j;
char * snps = 0;
Region * region = new Region
(
id,
lcbRegion.position,
lcbRegion.length,
lcbRegion.reverse,
snps
);
(*regions)[track] = region;
(*tracks[track])[id] = region;
if ( track == 0 )
{
totalLength += region->getLength();
}
}
lcbs[id].regions = regions;
}
for ( int i = 0; i < tracks.size(); i++ )
{
qSort(tracks[i]->begin(), tracks[i]->end(), Region::lessThan);
// determine total length
//
unsigned int length = 0;
//
for ( int j = 0; j < tracks[i]->size(); j++ )
{
length += (*tracks[i])[j]->getLength();
}
// assigned scaled
//
unsigned int position = 0;
//
for ( int j = 0; j < tracks[i]->size(); j++ )
{
(*tracks[i])[j]->setScaled
(
(float)position / length,
(float)(position + (*tracks[i])[j]->getLength()) / length
);
position += (*tracks[i])[j]->getLength();
}
}
snpMap.clear();
filters.resize(variantList.getFilterCount());
for ( int i = 0; i < variantList.getFilterCount(); i++ )
{
const VariantList::Filter & msgFilter = variantList.getFilter(i);
Filter & filter = filters[i];
filter.flag = msgFilter.flag;
filter.name = QString::fromStdString(msgFilter.name);
filter.description = QString::fromStdString(msgFilter.description);
}
snpCount = 0;
char refLast = 0;
int posLast;
gapsTotal = 0;
Gap gap;
snpColumns.resize(0);
gaps.resize(0);
for ( int i = 0; i < variantList.getVariantCount(); i++ )
{
const VariantList::Variant & msgSnp = variantList.getVariant(i);
long int refOffset = 0;
int refIndex = 0;
int position = msgSnp.position;
char charRef = msgSnp.reference; // TODO: fixed?
//char charRef = posLast == position ? '-' : referenceList.getReference(msgSnp.sequence).sequence[msgSnp.position];
while ( msgSnp.sequence > refIndex ) // - 1 OLD )
{
refOffset += referenceList.getReference(refIndex).sequence.length();
refIndex++;
}
position += refOffset;
if ( refLast == '-' && ( charRef != '-' || posLast != position ) )
{
gap.end = gap.startAbs + gapsTotal;
gap.offset = gapsTotal;
gaps.push_back(gap);
//gapsTotal += gap.end - gap.start + 1;
}
unsigned int filters = msgSnp.filters;
if ( charRef == '-' )
{
if ( refLast != '-' || posLast != position )
{
gap.start = position + gapsTotal + 1;
gap.startAbs = position;
}
gapsTotal++;
}
snpCount++;
snpColumns.resize(snpColumns.size() + 1);
snpMap.insert(snpMap.end(), std::pair<long long int, int>(position + gapsTotal, snpColumns.size() - 1));
SnpColumn & snpColumn = snpColumns[snpColumns.size() - 1];
snpColumn.position = position + gapsTotal;
// HACK for vcf; (fixed?)
//
snpColumn.ref = charRef;
snpColumn.filters = filters;
for ( unsigned int i = 0; i < msgSnp.alleles.length(); i++ )
{
char charQry = msgSnp.alleles.c_str()[i];
if ( charQry != snpColumn.ref )
{
Snp snp;
snp.track = i;
snp.snp = charQry;
snpColumn.snps.push_back(snp);
}
}
posLast = position;
refLast = charRef;
}
//totalLength = (*tracks[0])[tracks[0]->size() - 1]->getStart() + (*tracks[0])[tracks[0]->size() - 1]->getLength() + gapsTotal;
QString refSeq;
for ( int i = 0; i < referenceList.getReferenceCount(); i++ )
{
refSeq.append(QString::fromStdString(referenceList.getReference(i).sequence));
}
int coreSize = 0;
for ( int i = 0; i < lcbs.size(); i++ )
{
const Region * regionRef = (*lcbs[i].regions)[0];
int startGapped = getPositionGapped(regionRef->getStart() - 1) + 1;
int endGapped = getPositionGapped(regionRef->getStart() + regionRef->getLength()) - 1;
lcbs[i].startGapped = startGapped;
lcbs[i].lengthGapped = endGapped - startGapped + 1;
coreSize += regionRef->getLength();
}
core = (float)coreSize / refSeq.length();
qSort(lcbs.begin(), lcbs.end(), lcbLessThan);
totalLength = refSeq.length() + gapsTotal;
refSeqCount = referenceList.getReferenceCount();
if ( refSeqStarts )
{
delete [] refSeqStarts;
}
refSeqStarts = new long long int[refSeqCount];
long long int total = 0;
for ( int i = 0; i < refSeqCount; i++ )
{
refSeqStarts[i] = getPositionGapped(total);
total += referenceList.getReference(i).sequence.length();
}
if ( refSeqGapped )
{
delete [] refSeqGapped;
}
refSeqGapped = new char[totalLength];
int gapId = 0;
gapsTotal = 0;
for ( int i = 0; i < totalLength; i++ )
{
if ( gaps.size() && i == gaps[gapId].start )
{
while( i <= gaps[gapId].end )
{
refSeqGapped[i] = '-';
i++;
}
gapsTotal = gaps[gapId].offset;
if ( gapId < gaps.size() - 1 )
{
gapId++;
}
}
if ( i - gapsTotal < refSeq.length() )
{
refSeqGapped[i] = refSeq.at(i - gapsTotal).toLatin1(); // TODO: gap at pos 0?
}
}
if ( trackList.getTrackReference() > 0 )
{
setTrackReference(trackList.getTrackReference());
}
setFilterScale();
return true;
}
