             {
                 int u;
                 double e = calcEpsilon(referenceBases[k-1], queryBases[queryStart], inputQualities[queryStart]);
-//                fprintf(stderr, "read %d: referenceBases[%d-1] = %c inputQualities[%d] = %d queryBases[%d] = %c -> e = %.4f\n",
-//                        read_index,
-//                        k,
-//                        from_nvbio::iupac16_to_char(referenceBases[k-1]),
-//                        queryStart,
-//                        inputQualities[queryStart],
-//                        queryStart,
-//                        from_nvbio::iupac16_to_char(queryBases[queryStart]), e);
+//                printf("referenceBases[%d-1] = %c inputQualities[%d] = %d queryBases[%d] = %c -> e = %.4f\n",
+////                       read_index,
+//                       k,
+//                       from_nvbio::iupac16_to_char(referenceBases[k-1]),
+//                       queryStart,
+//                       inputQualities[queryStart],
+//                       queryStart,
+//                       from_nvbio::iupac16_to_char(queryBases[queryStart]), e);
 
                 u = set_u(bandWidth, 1, k);
 


                sum += fi[u] + fi[u+1] + fi[u+2];

    //            fprintf(stderr, "(%d,%d;%d): %.4f,%.4f,%.4f\n", i, k, u, fi[u], fi[u+1], fi[u+2]);
    //            fprintf(stderr, " .. u = %d v11 = %d v01 = %d v10 = %d e = %f\n", u, v11, v01, v10, e);
            }

            // rescale

        m[2*3+1] = 0.0;
        m[2*3+2] = GAP_EXTENSION_PROBABILITY;

//        printf("referenceStart = %u\n", referenceStart);
//        printf("queryStart = %u queryLen = %u\n", queryStart, queryLen);

        queryBases = batch.reads + idx.read_start + queryStart;
        referenceBases = ctx.reference.bases + referenceStart;
