Changeset 3356

Timestamp:

Nov 22, 2014, 2:34:04 PM (8 years ago)

Author:

Peter

Message:

refs #794. make test/pileup.cc compile with htslib

File:

• trunk/test/pileup.cc (modified) (6 diffs)

trunk/test/pileup.cc

@@ -49 +49 @@
 
 #ifdef YAT_HAVE_LIBBAM
+char seq_nt16(size_t x)
+{
+#if YAT_HAVE_HTSLIB
+  return seq_nt16_str[x];
+#elif HAVE_BAM_NT16_REV_TABLE
+  return bam_nt16_rev_table[x];
+#else
+  std::string table = "=ACMGRSVTWYHKDBN";
+  return table[c];
+#endif
+}
+
 void test1(test::Suite& suite, const std::string& fn)
 {
@@ -102 +114 @@
         continue;
       }
-      str += bam_nt16_rev_table[iter->sequence()];
+      str += seq_nt16(iter->sequence());
     }
 
@@ -169 +181 @@
       if (i->bam().pos()!=reads[1].pos())
         continue;
-      char nt = bam_nt16_rev_table[i->sequence()];
+      char nt = seq_nt16(i->sequence());
       if (nt != ref[plp.pos()-reads[0].pos()]) {
         error << "'" << nt << "' not equal '"
@@ -196 +208 @@
       ++count;
       suite.err() << count << "\n";
-      char nt = bam_nt16_rev_table[i->sequence()];
+      char nt = seq_nt16(i->sequence());
       if (nt != reads[1].sequence()[count-1])
         error << "nt: " << nt << " not as expected. count: " << count << "\n";
@@ -239 +251 @@
         continue;
       ++count;
-      char nt = bam_nt16_rev_table[i->sequence()];
+      char nt = seq_nt16(i->sequence());
       if (plp.pos() != reads[1].pos()+count-1)
         error << "count: " << count << " with pos: " << plp.pos() << "\n";
@@ -281 +293 @@
         continue;
       ++count;
-      char nt = bam_nt16_rev_table[i->sequence()];
+      char nt = seq_nt16(i->sequence());
       if (plp.skip_ref())
         error << count << " unexpected skip_ref\n";