(Generate patch)
# Line 782 | Line 782
782   //assumes N trimming was already done
783   //so a poly match should be very close to the end of the read
784   // -- find the initial match (seed)
785 < int lmin=GMAX((rlen-12), 0);
785 > int lmin=GMAX((rlen-16), 0);
786   int li;
787   for (li=rlen-4;li>lmin;li--) {
788     if (seedVal==*(int*)&(seq[li])) {
# Line 835 | Line 835
835         }
836      }
837   li=maxloc.pos;
838 < if ((maxloc.score>poly_minScore && ri>=rlen-3) ||
839 <    (maxloc.score==poly_minScore && ri==rlen-1) ||
840 <    (maxloc.score>(poly_minScore<<1) && ri>=rlen-6)) {
838 > if ((maxloc.score==poly_minScore && ri==rlen-1) ||
839 >    (maxloc.score>poly_minScore && ri>=rlen-3) ||
840 >    (maxloc.score>(poly_minScore*3) && ri>=rlen-8)) {
841    //trimming this li-ri match at 3' end
842      l3=li-1;
843      if (l3<0) l3=0;
# Line 856 | Line 856
856   //assumes N trimming was already done
857   //so a poly match should be very close to the end of the read
858   // -- find the initial match (seed)
859 < int lmax=GMIN(8, rlen-4);//how far from 5' end to look for 4-mer seeds
859 > int lmax=GMIN(12, rlen-4);//how far from 5' end to look for 4-mer seeds
860   int li;
861   for (li=0;li<=lmax;li++) {
862     if (seedVal==*(int*)&(seq[li])) {
# Line 911 | Line 911
911   ri=maxloc.pos;
912   if ((maxloc.score==poly_minScore && li==0) ||
913       (maxloc.score>poly_minScore && li<2)
914 <     || (maxloc.score>(poly_minScore<<1) && li<6)) {
914 >     || (maxloc.score>(poly_minScore*3) && li<8)) {
915      //adjust l5 to reflect this trimming of 5' end
916      l5=ri+1;
917      if (l5>rlen-1) l5=rlen-1;
# Line 1061 | Line 1061
1061   l5=0;
1062   l3=rseq.length()-1;
1063   #ifdef GDEBUG
1064 +   //rseq.reverse();
1065     GMessage(">%s\n", rname.chars());
1066     GMessage("%s\n",rseq.chars());
1067   #endif
# Line 1329 | Line 1330
1330          }
1331        if (l[i]!=0) {
1332          GStr s(&(l[i]));
1333 +      #ifdef GDEBUG
1334 +          //s.reverse();
1335 +      #endif
1337          continue;
1338          }
# Line 1341 | Line 1345
1345           s.nextToken(a3);
1346        a5.upper();
1347        a3.upper();
1348 +     #ifdef GDEBUG
1349 +     //   a5.reverse();
1350 +     //   a3.reverse();
1351 +     #endif