// Iteratively left-aligns the indels in the alignment until we have a stable
// realignment. Returns true on realignment success or non-realignment.
// Returns false if we exceed the maximum number of realignment iterations.
//
bool stablyLeftAlign(BAMALIGN& alignment, string referenceSequence, int maxiterations, bool debug) {
#ifdef VERBOSE_DEBUG
int mismatchesBefore = countMismatches(alignment, referenceSequence);
#endif
if (!leftAlign(alignment, referenceSequence, debug)) {
return true;
} else {
while (leftAlign(alignment, referenceSequence, debug) && --maxiterations > 0) {
LEFTALIGN_DEBUG("realigning ..." << endl);
}
#ifdef VERBOSE_DEBUG
int mismatchesAfter = countMismatches(alignment, referenceSequence);
if (mismatchesBefore != mismatchesAfter) {
cerr << alignment.QNAME << endl;
cerr << "ERROR: found " << mismatchesBefore << " mismatches before, but " << mismatchesAfter << " after left realignment!" << endl;
exit(1);
}
#endif
if (maxiterations <= 0) {
return false;
} else {
return true;
}
}
}
void test_countMismatches(char *a, char *b, int e)
{
int n;
if ((n=countMismatches(a,b)) == e) success++;
else { failure++; fprintf(stderr, "countMismatches(%s,%s) returned %d: expected %d\n", a,b,n,e); }
}