sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index b2322379d6eb0467c2e64ba5e98c28e6d604181c..90c13f8ee82722570d129d74874b519cc4ee9a60 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -24,8 +24,9 @@ public:
        vector<string> setParameters();\r
        string getCommandName()                 { return "filter.seqs";                 }\r
        string getCommandCategory()             { return "Sequence Processing"; }\r
-       string getOutputFileNameTag(string, string);\r
+       \r
        string getHelpString(); \r
+    string getOutputPattern(string);   \r
        string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }\r
        string getDescription()         { return "removes columns from alignments based on a criteria defined by the user"; }\r
        \r
@@ -152,7 +153,7 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
                        in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); \r
                }\r
                \r
-               pDataArray->count = pDataArray->end;\r
+               pDataArray->count = 0;\r
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process\r
                        \r
                        if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }\r
@@ -165,7 +166,7 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
                 if(pDataArray->trump != '*')                   {       pDataArray->F.doTrump(current);         }\r
                 if(pDataArray->m->isTrue(pDataArray->vertical) || pDataArray->soft != 0)       {       pDataArray->F.getFreqs(current);        }\r
                        }\r
-            \r
+            pDataArray->count++;\r
             //report progress\r
                        if((i) % 100 == 0){     pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }\r
                }\r
@@ -202,7 +203,7 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
                        in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); \r
                }\r
                \r
-               pDataArray->count = pDataArray->end;\r
+               pDataArray->count = 0;\r
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process\r
                        \r
                        if (pDataArray->m->control_pressed) { in.close(); out.close(); pDataArray->count = 1; return 1; }\r
@@ -220,7 +221,7 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
                 \r
                 out << '>' << seq.getName() << endl << filterSeq << endl;\r
             }\r
-            \r
+            pDataArray->count++;\r
             //report progress\r
                        if((i) % 100 == 0){     pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }\r
                }\r