* samtools-0.1.2-3

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index dbfc29576b57d9a7dbdee8c4f928c7334f468ce5..58e2be15384e010164274cce1ce8f15a5edbb4c3 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -87,13 +87,12 @@ static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
                min = g3;
                if (min > r->gl[0]) min = r->gl[0];
                if (min > r->gl[1]) min = r->gl[1];
-               g3 -= min;
                g2.ref_base = 0;
                g2.type = GLF_TYPE_INDEL;
                memset(g2.lk, 0, 10);
-               g2.lk[0] = r->gl[0] < 255? r->gl[0] : 255;
-               g2.lk[1] = r->gl[1] < 255? r->gl[1] : 255;
-               g2.lk[2] = g3 < 255? g3 : 255;
+               g2.lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
+               g2.lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
+               g2.lk[2] = g3 - min < 255? g3 - min : 255;
                *(int16_t*)(g2.lk + 3) = (int16_t)r->indel1;
                *(int16_t*)(g2.lk + 5) = (int16_t)r->indel2;
                g2.min_lk = min < 255? min : 255;