X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;fp=degapseqscommand.cpp;h=8f8a5c3901d845b27cdbeb5a3f0c34df0b587ce2;hb=80c3fe03a8fd1635d3ad7918ff00beb973449f50;hp=c6c4b5521fe35fa1984ecb56229a33c6c58c8163;hpb=dfae916a398508554d35c6b3c8002b69becb53be;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index c6c4b55..8f8a5c3 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -54,11 +54,21 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 					}
 	
 					ifstream in;
-					int ableToOpen = openInputFile(fastaFileNames[i], in);
+					int ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							fastaFileNames[i] = tryPath;
+						}
+					}
 					in.close();
 					
 					if (ableToOpen == 1) { 
-						m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+						m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 						//erase from file list
 						fastaFileNames.erase(fastaFileNames.begin()+i);
 						i--;