MonetDB: DVframework_bam - Updated bam library

[Robin Cijvat]

Changeset: 75127ac4ac30 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=75127ac4ac30
Modified Files:
        sql/backends/monet5/bam/bam_lib.c
Branch: DVframework_bam
Log Message:

Updated bam library


diffs (29 lines):

diff --git a/sql/backends/monet5/bam/bam_lib.c 
b/sql/backends/monet5/bam/bam_lib.c
--- a/sql/backends/monet5/bam/bam_lib.c
+++ b/sql/backends/monet5/bam/bam_lib.c
@@ -38,6 +38,16 @@ reverse_seq(str *ret, str *seq)
             case 'T': result[len-i-1] = 'A'; break;
             case 'C': result[len-i-1] = 'G'; break;
             case 'G': result[len-i-1] = 'C'; break;
+            case 'R': result[len-i-1] = 'Y'; break;
+            case 'Y': result[len-i-1] = 'R'; break;
+            case 'S': result[len-i-1] = 'S'; break;
+            case 'W': result[len-i-1] = 'W'; break;
+            case 'K': result[len-i-1] = 'M'; break;
+            case 'M': result[len-i-1] = 'K'; break;
+            case 'H': result[len-i-1] = 'D'; break;
+            case 'D': result[len-i-1] = 'H'; break;
+            case 'V': result[len-i-1] = 'B'; break;
+            case 'B': result[len-i-1] = 'V'; break;
             case 'N': result[len-i-1] = 'N'; break;
             default : throw(MAL, "reverse_seq", "Invalid character found in 
sequence: '%c'\n", (*seq)[i]);
         }
@@ -80,7 +90,7 @@ seq_length(int *ret, str *cigar)
         int nr_chars_read;
         if(sscanf(cigar_consumable, "%d%c%n", &cnt, &op, &nr_chars_read) != 2)
             throw(MAL, "seq_length", "Error parsing CIGAR string '%s'\n", 
*cigar);
-        if(op == 'M' || op == 'D' || op == '=') 
+        if(op == 'M' || op == 'D' || op == 'N' || op == '=' || op == 'X') 
             result += cnt;
         cigar_consumable += nr_chars_read;
     }
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