X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_color.c;fp=samtools%2Fbam_color.c;h=0000000000000000000000000000000000000000;hp=ce637f708db56de777e86f2f0ad50478fb1a6657;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/samtools/bam_color.c b/samtools/bam_color.c
deleted file mode 100644
index ce637f7..0000000
--- a/samtools/bam_color.c
+++ /dev/null
@@ -1,127 +0,0 @@
-#include <ctype.h>
-#include "bam.h"
-
-/*!
- @abstract     Get the color encoding the previous and current base
- @param b      pointer to an alignment
- @param i      The i-th position, 0-based
- @return       color
-
- @discussion   Returns 0 no color information is found.
- */
-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];
-}
-
-/*!
- @abstract     Get the color quality of the color encoding the previous and current base
- @param b      pointer to an alignment
- @param i      The i-th position, 0-based
- @return       color quality
-
- @discussion   Returns 0 no color information is found.
- */
-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)];
-}
-
-/*!
- @abstract     Get the color error profile at the give position    
- @param b      pointer to an alignment
- @return       the original color if the color was an error, '-' (dash) otherwise
-
- @discussion   Returns 0 no color information is found.
- */
-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.  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)]; 
-	}
-	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;
-	}
-}