X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimoligos.cpp;h=ddc1053f50d3eba28064907e4c6f0a60a958b3ee;hp=504a8b59e35b2e99567e7085ccd964b43d8d8361;hb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7;hpb=b8ff3bca0560a53832723f4621fcddef7ec4e499

diff --git a/trimoligos.cpp b/trimoligos.cpp
index 504a8b5..ddc1053 100644
--- a/trimoligos.cpp
+++ b/trimoligos.cpp
@@ -855,6 +855,8 @@ int TrimOligos::stripPairedBarcode(Sequence& seq, QualityScores& qual, int& grou
                 break;
             }
             
+            if (rawSeq.length() < (foligo.length() + roligo.length())) {  success = pdiffs + 10; break; }
+            
             if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
                 group = it->first;
                 string trimmedSeq = rawSeq.substr(foligo.length()); //trim forward barcode
@@ -1078,6 +1080,8 @@ int TrimOligos::stripPairedPrimers(Sequence& seq, QualityScores& qual, int& grou
                 break;
             }
             
+            if (rawSeq.length() < (foligo.length() + roligo.length())) {  success = pdiffs + 10; break; }
+            
             if((compareDNASeq(foligo, rawSeq.substr(0,foligo.length()))) && (compareDNASeq(roligo, rawSeq.substr(rawSeq.length()-roligo.length(),roligo.length())))) {
                 group = it->first;
                 if (!keepForward) {