Fix to prevent long stretches of Ns to be mistaken for indels; Always output the...

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 5142b3e100aa96a7ab598a95b9953aa4c6034289..11cd371978e6e654987d35c35dd6465539a22523 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -161,6 +161,11 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                if (j > max_rd_len) max_rd_len = j;
                        }
                }
+        // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
+        //  check the number of N's in the sequence. TODO: this may not be the best place and the best way of doing it
+        int nN=0; for (i=0; i<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
+        if ( nN*2>i ) return -1;
+
                ks_introsort(uint32_t, m, aux);
                // squeeze out identical types
                for (i = 1, n_types = 1; i < m; ++i)

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index a380484310ccd7dc0ee72f922ba9f97aef6be80a..15735af32cad689dccc41ea186caaa7bf2db3d72 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -193,24 +193,21 @@ void bcf_p1_destroy(bcf_p1aux_t *ma)
 
 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
 {
-       int i, j;
-       long *p, tmp;
-       p = alloca(b->n_alleles * sizeof(long));
-       memset(p, 0, sizeof(long) * b->n_alleles);
+       int i, j, imax=0;
        for (j = 0; j < ma->n; ++j) {
                const uint8_t *pi = ma->PL + j * ma->PL_len;
                double *pdg = ma->pdg + j * 3;
                pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
-               for (i = 0; i < b->n_alleles; ++i)
-                       p[i] += (int)pi[(i+1)*(i+2)/2-1];
+        int ib,ia=0,n=(b->n_alleles+1)*b->n_alleles/2;
+        for (i=0; i<n;) {
+            for (ib=0; ib<=ia; ib++) {
+                if ( pi[i]==0 && ia>imax ) imax=ia;
+                i++;
+            }
+            ia++;
+        }
        }
-       for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
-       for (i = 1; i < b->n_alleles; ++i) // insertion sort
-               for (j = i; j > 0 && p[j] < p[j-1]; --j)
-                       tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
-       for (i = b->n_alleles - 1; i >= 0; --i)
-               if ((p[i]&0xf) == 0) break;
-       return i;
+       return imax;
 }
 
 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)