+ //sometimes the parent regions do not meet, for example region 1 may end at 1000 and region 2 starts at 1100.
+ //we don't want to loose length so in this case we will leave query alone
+ if (i != 0) {
+ int space = parents[i].nastRegionStart - parents[i-1].nastRegionEnd - 1;
+ if (space > 0) { //they don't meet and we need to add query piece
+ string q = qAligned.substr(parents[i-1].nastRegionEnd+1, space);
+ newQuery += q;
+ }
+ }
+