- in >> tempNum; gobble(in); num += tempNum;
- for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } gobble(in);
- for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } gobble(in);
- for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } gobble(in);
- for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } gobble(in);
- for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } gobble(in);
+ string tempFilterString;
+
+ in >> tempNum; m->gobble(in); num += tempNum;
+
+ in >> tempFilterString;
+ F.mergeFilter(tempFilterString);
+
+ for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } m->gobble(in);
+ for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } m->gobble(in);
+ for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } m->gobble(in);
+ for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } m->gobble(in);
+ for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in);