Merge commit 'upstream/0.5'

[pysam.git] / samtools / bam_color.c

diff --git a/samtools/bam_color.c b/samtools/bam_color.c
deleted file mode 100644 (file)
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;
-       }
-}