Merge remote-tracking branch 'mothur/master'

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index f37c56d3e59bf3d010397ad6c1262c1071adc1ff..3c14d55163ab260db87b7a35c271e664b7584945 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1958,7 +1958,7 @@
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
                        attributes = {
-                               LastUpgradeCheck = 0420;
+                               LastUpgradeCheck = 0460;
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
@@ -2353,6 +2353,7 @@
                                GCC_OPTIMIZATION_LEVEL = 3;
                                "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;
+                               SDKROOT = macosx;
                                SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                        };
@@ -2369,6 +2370,7 @@
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_UNUSED_VALUE = YES;
                                PRODUCT_NAME = mothur;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                        };
                        name = Release;
@@ -2405,7 +2407,7 @@
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx10.8;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
@@ -2443,7 +2445,7 @@
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx10.8;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                        };
                        name = Release;

diff --git a/command.hpp b/command.hpp
index 48dcf283c8874c8168ac6cf48748bf80851caef3..37186529ab1f75e5747138d74f976c5df3c1bbe9 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -3,7 +3,7 @@
 //test2
 /*
  *  command.h
- *  
+ *  nast
  *
  *  Created by Pat Schloss on 10/23/08.
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 0a6eae93df72e8556554bef32c5a52074a4d0a54..e48d50794d15b4b77dae6a15134d9bec54c8a911 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -673,10 +673,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                int numSeqs = 0;
                
                map<string, int>::iterator it;
-               qScoreErrorMap['m'].assign(41, 0);
-               qScoreErrorMap['s'].assign(41, 0);
-               qScoreErrorMap['i'].assign(41, 0);
-               qScoreErrorMap['a'].assign(41, 0);
+               qScoreErrorMap['m'].assign(101, 0);
+               qScoreErrorMap['s'].assign(101, 0);
+               qScoreErrorMap['i'].assign(101, 0);
+               qScoreErrorMap['a'].assign(101, 0);
                
                errorForward['m'].assign(maxLength,0);
                errorForward['s'].assign(maxLength,0);
@@ -712,8 +712,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        qualForwardMap.resize(maxLength);
                        qualReverseMap.resize(maxLength);
                        for(int i=0;i<maxLength;i++){
-                               qualForwardMap[i].assign(41,0);
-                               qualReverseMap[i].assign(41,0);
+                               qualForwardMap[i].assign(101,0);
+                               qualReverseMap[i].assign(101,0);
                        }       
                }
                else if(qFileName != "" && !aligned){
@@ -724,8 +724,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        qualForwardMap.resize(maxLength);
                        qualReverseMap.resize(maxLength);
                        for(int i=0;i<maxLength;i++){
-                               qualForwardMap[i].assign(41,0);
-                               qualReverseMap[i].assign(41,0);
+                               qualForwardMap[i].assign(101,0);
+                               qualReverseMap[i].assign(101,0);
                        }       
         }
         
@@ -1271,7 +1271,7 @@ void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
                outputNames.push_back(errorQualityFileName);  outputTypes["errorquality"].push_back(errorQualityFileName);
 
                errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
-               for(int i=0;i<41;i++){
+               for(int i=0;i<101;i++){
                        errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
                }
                errorQualityFile.close();