Exemple #1
0
// 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;
        }

    }

}
Exemple #2
0
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); }
}