if (alignSeqs[j].active) { //this sequence has not been merged yet
string jBases = alignSeqs[j].seq.getUnaligned();
-
+
if (isFragment(iBases, jBases)) {
//merge
alignSeqs[i].names += ',' + alignSeqs[j].names;
int percentDiff = floor((seq2.length() * (percent / 100.0)));
if (percentDiff < totalDiffs) { totalDiffs = percentDiff; }
}
-
+
Alignment* alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (seq1.length()+totalDiffs+1));
//use needleman to align
}
if (numDiffs <= totalDiffs) { fragment = true; }
+
}
return fragment;