Changeset 2972 for branches/0.10-stable/yat/omic/BamRead.cc

Timestamp:

Jan 26, 2013, 7:53:56 AM (10 years ago)

Author:

Peter

Message:

refs #745. Implement a workaround when bam_nt16_rev_table is not
available in -lbam.

File:

• branches/0.10-stable/yat/omic/BamRead.cc (modified) (1 diff)

branches/0.10-stable/yat/omic/BamRead.cc

@@ -149 +149 @@
   std::string BamRead::sequence(void) const
   {
-    // FIXME bam_nt16_rev_table not available in old lbam
     std::string result(sequence_length(), ' ');
+#ifdef HAVE_BAM_NT16_REV_TABLE
     for (size_t i=0; i<result.size(); ++i)
       result[i] = bam_nt16_rev_table[sequence(i)];
+#else
+    std::string table = "=ACMGRSVTWYHKDBN";
+    for (size_t i=0; i<result.size(); ++i)
+      result[i] = table[sequence(i)];
+#endif
     return result;
   }