X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=93adb7bf53b280892715411c66aedcf15b5c0df3;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=2c6fec8d8d1082ea270f5e2c2a8832a7b57033a4;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 2c6fec8..93adb7b 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -15,6 +15,7 @@
 #include "chimera.h"
 #include "chimeraslayer.h"
 #include "sequenceparser.h"
+#include "sequencecountparser.h"
 
 /***********************************************************/
 
@@ -27,6 +28,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.slayer";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
@@ -50,12 +52,14 @@ private:
 	int divideInHalf(Sequence, string&, string&);
 	map<string, int> sortFastaFile(string, string);
 	map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
+    int sortFastaFile(vector<Sequence>&, map<string, int>&, string newFile);
 	string getNamesFile(string&);
 	//int setupChimera(string,);
 	int MPIExecute(string, string, string, string, map<string, int>&);
-	int deconvoluteResults(SequenceParser*, string, string, string);
+	int deconvoluteResults(map<string, string>&, string, string, string);
 	map<string, int> priority;
 	int setUpForSelfReference(SequenceParser*&, map<string, string>&, map<string, map<string, int> >&, int);
+    int setUpForSelfReference(SequenceCountParser*&, map<string, string>&, map<string, map<string, int> >&, int);
 	int driverGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
 	int createProcessesGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
 	int MPIExecuteGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
@@ -65,8 +69,8 @@ private:
 	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
 	#endif
 
-	bool abort, realign, trim, trimera, save;
-	string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
+	bool abort, realign, trim, trimera, save, hasName, hasCount;
+	string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
 	int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
 	float divR;