# HG changeset patch
# User greg
# Date 1515780767 18000
# Node ID 26c26cb321372bc95a12fc74285e196a72de6ee0
# Parent  9d34f7e6d80c845565aedb08bad70916dd437971
Uploaded

diff -r 9d34f7e6d80c -r 26c26cb32137 ideas.R
--- a/ideas.R	Fri Jan 12 11:53:17 2018 -0500
+++ b/ideas.R	Fri Jan 12 13:12:47 2018 -0500
@@ -326,20 +326,32 @@
 cmd = paste(cmd, "-thread", opt$thread, sep=" ");
 
 if (is.null(opt$training_iterations)) {
-    cmd = paste(cmd, "-o", output_base_name, sep=" ");
-    cmd = add_output_redirect(cmd, opt$save_ideas_log, opt$output_log, default_log_name);
-    run_cmd(cmd, opt$save_ideas_log, opt$output_log, default_log_name);
+    final_cmd = paste(cmd, "-o", output_base_name, sep=" ");
+    final_cmd = add_output_redirect(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
+    run_cmd(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
 } else {
+    output_para0 = paste(output_base_name, ".para0", sep="");
+    output_profile0 = paste(output_base_name, ".profile0", sep="");
     for (i in 1:opt$training_iterations) {
-        cmd = paste(cmd, "-o", paste(output_base_name, ".tmp.", i, sep=""), sep=" ");
-        cmd = add_output_redirect(cmd, opt$save_ideas_log, opt$output_log, default_log_name);
-        run_cmd(cmd, opt$save_ideas_log, opt$output_log, default_log_name);
+        final_cmd = paste(cmd, "-o", paste(output_base_name, ".tmp.", i, sep=""), sep=" ");
+        final_cmd = add_output_redirect(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
+        run_cmd(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
     }
     tpara = combine_state(paste(output_base_name, ".tmp.", (1:opt$training_iterations), ".para", sep=""), mycut=0.5);
     para = tpara$para;
-    write.table(tpara$profile, paste(output_base_name, ".profile0", sep=""), quote=F, row.names=F, col.names=F);
+    write.table(tpara$profile, output_profile0, quote=F, row.names=F, col.names=F);
     para = apply(para, 1, function(x){paste(x, collapse=" ")});
     para = c(readLines(paste(output_base_name, ".tmp.1.para", sep=""), n=1), para);
-    output_para0 = paste(output_base_name, ".para0", sep="");
     writeLines(para, output_para0);
+    cmd = c(cmd, "-otherpara", output_para0, output_profile0);
+    if (length(which(cmd == "-G")) == 0) {
+        cmd = c(cmd, "-G", length(para)-1);
+    } else {
+        tt = which(cmd == "-G");
+        cmd[tt + 1] = length(para)-1;
+    }
+    tt = which(cmd == '-C');
+    if(length(tt)>0) {
+        cmd = cmd[-c(tt, tt+1)];
+    }
 }