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opticall  committed 76a3850

changed -noblank default option to -blank

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  • Parent commits a2705f0

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File opticall/opticall.cpp

 	//char * output_prob_ext = ".probs";
 	//char * output_call_ext = ".calls";
 
-	string version = "0.6.2";
+	string version = "0.6.3";
 	cout << "opticall version " << version << endl;
 	cout << "thank you for choosing opticall for your genotyping needs" << endl;
 
 	double resc_threshhold = 5*1e-15;
 	double initial_outliers_numsds = 3;
 	bool nonorm = false;
-	bool noblank = false;
+	bool noblank = true;
 	bool meanintfilter = false;
 	bool outliers_only = false;
 	string chrom_type = "A";
 			cout << "optiCall will output samples with outlying mean-intensity across SNPs, then stop. No Calling will be performed." << endl;
 			meanintfilter = true;
 			outliers_only = true;
+		} else if (string(argv[i]) == "-blank") {
+			cout << "turning on HWE based SNP blanking" << endl;
+			noblank = false;
 		} else if (string(argv[i]) == "-noblank") {
 			cout << "turning off HWE based SNP blanking" << endl;
 			noblank = true;