* samtools-0.1.4-2 (r316)

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index c6c9af7dee454ed91cd75363470473405d7c97ea..95cd2b5f68f748f1412a8dc089784f3069d972c5 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -108,6 +108,7 @@ bam_maqcns_t *bam_maqcns_init()
        bm->theta = 0.85;
        bm->n_hap = 2;
        bm->eta = 0.03;
+       bm->cap_mapQ = 60;
        return bm;
 }
 
@@ -160,6 +161,7 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
        rms = 0;
        for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
                uint32_t info = bm->aux->info[j];
+               int tmp;
                if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | (info&0xffffff);
                k = info>>16&7;
                if (info>>24 > 0) {
@@ -168,7 +170,8 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
                        if (w[k] < 0xff) ++w[k];
                        ++b->c[k&3];
                }
-               rms += (int)(info&0x7f) * (info&0x7f);
+               tmp = (int)(info&0x7f) < bm->cap_mapQ? (int)(info&0x7f) : bm->cap_mapQ;
+               rms += tmp * tmp;
        }
        b->rms_mapQ = (uint8_t)(sqrt((double)rms / n) + .499);
        // rescale ->c[]