X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=58e2be15384e010164274cce1ce8f15a5edbb4c3;hb=c7387993bba745f3cbcff7c400583d68771a2572;hp=dbfc29576b57d9a7dbdee8c4f928c7334f468ce5;hpb=a2ef036000d869f35ec58e66e5f2a748cdc2d128;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index dbfc295..58e2be1 100644
--- 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;