fix for specificity calculation for sam format (similar to commit 98b…

…c2 for csv format

include/genomics/printer.hpp

@@ -135,9 +135,14 @@ namespace genomics {
               // because the match may well have been found using
               // an alternate PAM. The relevant PAM to consider for
               // CFD calculations is found at the end of the match.
-              std::string pam = match_sequence.substr(20, 3);
-
-              if ((match.mismatches == 0) && (pam.substr(1, 2) == "GG"))
+              std::string pam;
+              if (match_sequence.length() < 20) {
+                pam = "";
+              } else {
+                pam = match_sequence.substr(20, 3);
+              }
+
+              if ((match.mismatches == 0) && (pam.length() == 3) && (pam.substr(1, 2) == "GG"))
                 perfect_match = true;
 
               coordinates c;