Merge branch 'jh_nov2018' into new_hts

Author: julianhess

src/GenomicRegion.cpp

@@ -3,6 +3,9 @@
 #include <cassert>
 #include <stdexcept>
 #include <climits>
+#ifdef HAVE_C11
+#include <regex>
+#endif
 
 // 4 billion
 #define END_MAX 4000000000
@@ -275,6 +278,16 @@ int32_t GenomicRegion::DistanceBetweenEnds(const GenomicRegion &gr) const {
       return;
     } else {
       chr = hdr.Name2ID(tchr); //bam_name2id(hdr.get(), tchr.c_str());
+
+      // if tchr was not found in sequence dictionary, it's possible that we're 
+      // specifying our contigs in b37 style whereas dict is hg** style;
+      // let's attempt to automatically convert [0-9XY]+ -> chr[0-9XY]+
+#ifdef HAVE_C11
+      static std::regex b37_regex("[0-9XY]+");
+      if(chr == -1 && std::regex_match(tchr, b37_regex)) {
+	 chr = hdr.Name2ID("chr" + tchr);
+      }
+#endif
     }
   }
 }