Merge branch 'upstream'

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 464288ae7da0ac74f1443bbb55c03684927cb391..f36b0ee2ab443affe0635866a8d593c5cb54fdf7 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -439,7 +439,7 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                }
                                if (score[i*n+j] < s) score[i*n+j] = s; // choose the higher of the two scores
                                if (pscore[i*n+j] > ps) pscore[i*n+j] = ps;
-                               if (types[i] != 0) score[i*n+j] -= mi->indel_err;
+                               //if (types[i] != 0) score[i*n+j] -= mi->indel_err;
                                //printf("%d, %d, %d, %d, %d, %d, %d\n", p->b->core.pos + 1, seg.qbeg, i, types[i], j,
                                //         score[i*n+j], pscore[i*n+j]);
                        }
@@ -499,6 +499,15 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                if (s1 > s2) ret->gl[0] += s1 - s2 < mi->q_indel? s1 - s2 : mi->q_indel;
                                else ret->gl[1] += s2 - s1 < mi->q_indel? s2 - s1 : mi->q_indel;
                        }
+                       // write cnt_ref and cnt_ambi
+                       if (max1_i != 0 && max2_i != 0) {
+                               for (j = 0; j < n; ++j) {
+                                       int diff1 = score[j] - score[max1_i * n + j];
+                                       int diff2 = score[j] - score[max2_i * n + j];
+                                       if (diff1 > 0 && diff2 > 0) ++ret->cnt_ref;
+                                       else if (diff1 == 0 || diff2 == 0) ++ret->cnt_ambi;
+                               }
+                       }
                }
                free(score); free(pscore); free(ref2); free(inscns);
        }