Merge commit 'upstream/0.5'

[pysam.git] / samtools / bam_color.c.pysam.c

diff --git a/samtools/bam_color.c.pysam.c b/samtools/bam_color.c.pysam.c
new file mode 100644 (file)
index 0000000..f71c65f
--- /dev/null
+++ b/samtools/bam_color.c.pysam.c
@@ -0,0 +1,129 @@
+#include "pysam.h"
+
+#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;
+       }
+}