X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_color.c;h=8b86e2fb6fb0a328b4a903e6dd2d463c3a0114c9;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=75aedd603a1798e85a40c982dd9392ee2a3e5b3f;hpb=1a23a35867ee992dcffcf3d17df2b7d41732f33b;p=samtools.git

diff --git a/bam_color.c b/bam_color.c
index 75aedd6..8b86e2f 100644
--- a/bam_color.c
+++ b/bam_color.c
@@ -19,8 +19,14 @@ char bam_aux_getCSi(bam1_t *b, int i)
 
 	cs = bam_aux2Z(c);
 	// adjust for strandedness and leading adaptor
-	if(bam1_strand(b)) i = strlen(cs) - 1 - i;
-	else i++;
+	if(bam1_strand(b)) {
+	    i = strlen(cs) - 1 - i;
+	    // adjust for leading hard clip
+	    uint32_t cigar = bam1_cigar(b)[0];
+	    if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+		i -= cigar >> BAM_CIGAR_SHIFT;
+	    }
+	} else { i++; }
 	return cs[i];
 }
 
@@ -42,7 +48,14 @@ char bam_aux_getCQi(bam1_t *b, int i)
 
 	cq = bam_aux2Z(c);
 	// adjust for strandedness
-	if(bam1_strand(b)) i = strlen(cq) - 1 - i;
+	if(bam1_strand(b)) {
+	    i = strlen(cq) - 1 - i;
+	    // adjust for leading hard clip
+	    uint32_t cigar = bam1_cigar(b)[0];
+	    if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+		i -= (cigar >> BAM_CIGAR_SHIFT);
+	    }
+	}
 	return cq[i];
 }
 
@@ -98,10 +111,15 @@ char bam_aux_getCEi(bam1_t *b, int i)
 	// adjust for strandedness and leading adaptor
 	if(bam1_strand(b)) { //reverse strand
 		cs_i = strlen(cs) - 1 - i;
+		// adjust for leading hard clip
+		uint32_t cigar = bam1_cigar(b)[0];
+		if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+			cs_i -= cigar >> BAM_CIGAR_SHIFT;
+		}
 		// get current color
 		cur_color = cs[cs_i];
-		// get previous base
-		prev_b = (0 == cs_i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
+		// get previous base.  Note: must rc adaptor
+		prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
 		// get current base
 		cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; 
 	}