--- a/coverage_plot.r	Mon Jun 03 12:29:29 2013 -0400
+++ b/coverage_plot.r	Mon Jul 15 10:47:35 2013 -0400
@@ -1,19 +1,22 @@
-x <- read.table('coverage2.txt', skip=1, sep='\t')
+args <- commandArgs(TRUE);
+output_file <- args[1];
+
+x <- read.table('coverage2.txt', skip=1, sep='\t');
 
-individuals <- dim(x)[1]
-max_cov <- dim(x)[2] - 2
-max_val <- max(x[-1]) / 100
-colors <- rainbow(individuals)
+individuals <- dim(x)[1];
+max_cov <- dim(x)[2] - 2;
+max_val <- max(x[-1]) / 100;
+colors <- rainbow(individuals);
 
-line_width = 3
-xt = t(x)
+line_width = 3;
+xt = t(x);
 
-xvals <- c(0:max_cov)
-values <- as.numeric(as.vector(xt[,1][-1]))/100
+xvals <- c(0:max_cov);
+values <- as.numeric(as.vector(xt[,1][-1]))/100;
 
-pdf(file='coverage.pdf', onefile=TRUE, width=10, height=6);
+pdf(file=output_file, onefile=TRUE, width=10, height=6);
 
-plot(xvals, values, type='l', ylim=c(0, max_val), xlim=c(0, max_cov), col=colors[1], lwd=line_width, xlab="Coverage", ylab="Proportion")
+plot(xvals, values, type='l', ylim=c(0, max_val), xlim=c(0, max_cov), col=colors[1], lwd=line_width, xlab="Coverage", ylab="Proportion");
 
 if (individuals > 1) {
     for (i in 2:individuals) {
@@ -23,9 +26,7 @@
 }
 
 
-names <- as.vector(t(x[1]))
-legend(x='topright', legend=names, fill=colors, bty='n')
+names <- as.vector(t(x[1]));
+legend(x='topright', legend=names, fill=colors, bty='n');
 
-dev.off()
-
-
+dev.off();