Alternative model for multiallelic and rare-variant calling. Proof-of-principle imple...

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 502d832455fb09bd2b9a2e1a1b21d077cafd869c..ed78ea6c7048fb9d21248cb4812726c77e3afd45 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -195,6 +195,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        for (i = 0; i < n; ++i)
                for (j = 0; j < 4; ++j)
                        qsum[j] += calls[i].qsum[j];
+    int qsum_tot=0;
+    for (j=0; j<4; j++) qsum_tot += qsum[j];
        for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
        // find the top 2 alleles
        for (i = 1; i < 4; ++i) // insertion sort
@@ -206,9 +208,15 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        call->a[0] = ref4;
        for (i = 3, j = 1; i >= 0; --i) {
                if ((qsum[i]&3) != ref4) {
-                       if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
+                       if (qsum[i]>>2 != 0) 
+            {
+                call->qsum[j] = (float)(qsum[i]>>2)/qsum_tot;
+                call->a[j++]  = qsum[i]&3;
+            }
                        else break;
                }
+        else 
+            call->qsum[0] = (float)(qsum[i]>>2)/qsum_tot;
        }
        if (ref_base >= 0) { // for SNPs, find the "unseen" base
                if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
@@ -311,6 +319,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
                if (i) kputc(',', &s);
                kputw(bc->anno[i], &s);
        }
+    ksprintf(&s,";QS=%f,%f,%f,%f", bc->qsum[0],bc->qsum[1],bc->qsum[2],bc->qsum[3]);
     if (bc->vdb != 1)
         ksprintf(&s, ";VDB=%.4f", bc->vdb);
        kputc('\0', &s);