X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_aux.c;fp=bam_aux.c;h=a63e2aeadccf35e95b786097cd33394cb31a7a06;hb=1a23a35867ee992dcffcf3d17df2b7d41732f33b;hp=f36bc2351ee0c74ad87f877f7a3797e3281461d8;hpb=63e8f525a5fd57be4c3471739a3996016e0c25f9;p=samtools.git

diff --git a/bam_aux.c b/bam_aux.c
index f36bc23..a63e2ae 100644
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -226,107 +226,3 @@ void bam_strmap_destroy(void *rg2lib)
 	}
 	kh_destroy(r2l, h);
 }
-
-/*** The following routines were implemented by Nils Homer for color-space support in tview ***/
-
-char bam_aux_getCSi(bam1_t *b, int i)
-{
-	uint8_t *c = bam_aux_get(b, "CS");
-	char *cs = NULL;
-
-	// return the base if the tag was not found
-	if(0 == c) return 0;
-
-	cs = bam_aux2Z(c);
-	// adjust for strandedness and leading adaptor
-	if(bam1_strand(b)) i = strlen(cs) - 1 - i;
-	else i++;
-	return cs[i];
-}
-
-char bam_aux_getCQi(bam1_t *b, int i)
-{
-	uint8_t *c = bam_aux_get(b, "CQ");
-	char *cq = NULL;
-	
-	// return the base if the tag was not found
-	if(0 == c) return 0;
-
-	cq = bam_aux2Z(c);
-	// adjust for strandedness
-	if(bam1_strand(b)) i = strlen(cq) - 1 - i;
-	return cq[i];
-}
-
-char bam_aux_nt2int(char a)
-{
-	switch(toupper(a)) {
-		case 'A':
-			return 0;
-			break;
-		case 'C':
-			return 1;
-			break;
-		case 'G':
-			return 2;
-			break;
-		case 'T':
-			return 3;
-			break;
-		default:
-			return 4;
-			break;
-	}
-}
-
-char bam_aux_ntnt2cs(char a, char b)
-{
-	a = bam_aux_nt2int(a);
-	b = bam_aux_nt2int(b);
-	if(4 == a || 4 == b) return '4';
-	return "0123"[(int)(a ^ b)];
-}
-
-char bam_aux_getCEi(bam1_t *b, int i)
-{
-	int cs_i;
-	uint8_t *c = bam_aux_get(b, "CS");
-	char *cs = NULL;
-	char prev_b, cur_b;
-	char cur_color, cor_color;
-
-	// return the base if the tag was not found
-	if(0 == c) return 0;
-	
-	cs = bam_aux2Z(c);
-
-	// adjust for strandedness and leading adaptor
-	if(bam1_strand(b)) { //reverse strand
-		cs_i = strlen(cs) - 1 - i;
-		// 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 current base
-		cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; 
-	}
-	else {
-		cs_i=i+1;
-		// get current color
-		cur_color = cs[cs_i];
-		// get previous base
-		prev_b = (0 == i) ? 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)];
-	}
-
-	// corrected color
-	cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
-
-	if(cur_color == cor_color) { 
-		return '-';
-	}
-	else {
-		return cur_color;
-	}
-}