Sorry. The old Makefile is for PDCurses...

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 95cd2b5f68f748f1412a8dc089784f3069d972c5..464288ae7da0ac74f1443bbb55c03684927cb391 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -213,6 +213,25 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
                        if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
        }
 
+       { // fix p[k<<2|k]
+               float max1, max2, min1, min2;
+               int max_k, min_k;
+               max_k = min_k = -1;
+               max1 = max2 = -1.0; min1 = min2 = 1e30;
+               for (k = 0; k < 4; ++k) {
+                       if (b->esum[k] > max1) {
+                               max2 = max1; max1 = b->esum[k]; max_k = k;
+                       } else if (b->esum[k] > max2) max2 = b->esum[k];
+               }
+               for (k = 0; k < 4; ++k) {
+                       if (p[k<<2|k] < min1) {
+                               min2 = min1; min1 = p[k<<2|k]; min_k = k;
+                       } else if (p[k<<2|k] < min2) min2 = p[k<<2|k];
+               }
+               if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
+                       p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
+       }
+
        // convert necessary information to glf1_t
        g->ref_base = ref_base; g->max_mapQ = b->rms_mapQ;
        g->depth = n > 16777215? 16777215 : n;