// DEBUG
void checkNode(Node* node) {
PassageMarkerI marker1 = getMarker(node);
if (marker1 == NULL_IDX)
return;
PassageMarkerI marker2 = getNextInNode(marker1);
if (marker2 == NULL_IDX)
return;
if (getStartOffset(marker1) == getStartOffset(marker2))
abort();
if (getFinishOffset(marker1) == getFinishOffset(marker2))
abort();
printf(">>>> Node %li\n", (long) getNodeID(node));
printf("Marker1: %li - %li > %li (%li) \n", (long) getStartOffset(marker1), (long) getPassageMarkerLength(marker1), (long) (getNodeLength(node) - getFinishOffset(marker1)), (long) getFinishOffset(marker1));
printf("%s\n", readPassageMarker(marker1));
printf("Marker2: %li - %li > %li (%li) \n", (long) getStartOffset(marker2), (long) getPassageMarkerLength(marker2), (long) (getNodeLength(node) - getFinishOffset(marker2)), (long) getFinishOffset(marker2));
printf("%s\n", readPassageMarker(marker2));
if (getStartOffset(marker1) < getNodeLength(node) - getFinishOffset(marker2)
&& getStartOffset(marker2) < getNodeLength(node) - getFinishOffset(marker1)) {
//abort();
;
}
}
static TightString *readNegativePassageMarker(PassageMarkerI marker,
TightString ** seqs)
{
Coordinate index;
Nucleotide nucleotide;
TightString *tString =
seqs[getAbsolutePassMarkerSeqID(marker) - 1];
TightString *res = newTightString(getPassageMarkerLength(marker));
for (index = 0; index < getPassageMarkerLength(marker); index++) {
nucleotide =
getNucleotide(getPassageMarkerStart(marker) - index,
tString);
#ifndef COLOR
writeNucleotideAtPosition(3 - nucleotide, index, res);
#else
writeNucleotideAtPosition(nucleotide, index, res);
#endif
}
return res;
}
static TightString *readPositivePassageMarker(PassageMarkerI marker,
TightString ** seqs,
int WORDLENGTH)
{
Coordinate index;
Nucleotide nucleotide;
TightString *tString =
seqs[getPassageMarkerSequenceID(marker) - 1];
TightString *res = newTightString(getPassageMarkerLength(marker));
for (index = 0; index < getLength(tString); index++) {
nucleotide =
getNucleotide(getPassageMarkerStart(marker) + index +
WORDLENGTH - 1, tString);
writeNucleotideAtPosition(nucleotide, index, res);
}
return res;
}
static void adjustShortReads(Node * target, PassageMarkerI pathMarker)
{
ShortReadMarker *targetArray, *marker;
IDnum targetLength, index;
Coordinate position, nodeLength;
if (!readStartsAreActivated(graph))
return;
targetArray = getNodeReads(getTwinNode(target), graph);
targetLength = getNodeReadCount(getTwinNode(target), graph);
nodeLength = getPassageMarkerLength(pathMarker);
for (index = 0; index < targetLength; index++) {
marker = getShortReadMarkerAtIndex(targetArray, index);
position = getShortReadMarkerPosition(marker);
position += nodeLength;
setShortReadMarkerPosition(marker, position);
}
}