Update URLs to Github

Author: lishen

bin/ngs.plot.r

@@ -26,7 +26,7 @@ source(file.path(progpath, 'lib', 'coverage.r'))
 
 # Deal with command line arguments.
 cmd.help <- function(){
-    cat("\nVisit http://code.google.com/p/ngsplot/wiki/ProgramArguments101 for details\n")
+    cat("\nVisit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details\n")
     cat(paste("Version:", ngsplot.version, sep=" "))
     cat("\nUsage: ngs.plot.r -G genome -R region -C [cov|config]file\n")
     cat("                  -O name [Options]\n")

bin/plotCorrGram.r

@@ -8,7 +8,7 @@
 #
 
 cmd.help <- function(){
-    cat("\nVisit http://code.google.com/p/ngsplot for details\n")
+    cat("\nVisit https://github.com/shenlab-sinai/ngsplot for details\n")
     cat("\nUsage: plotCorrGram.r -I ngsplot_output.zip -O output_name [Options]\n")
     cat("\n## Mandatory parameters:\n")
     cat("  -I   Result zip file created by ngs.plot.\n")

bin/replot.r

@@ -17,7 +17,7 @@ source(file.path(progpath, 'lib', 'parse.args.r'))
 source(file.path(progpath, 'lib', 'plotlib.r'))
 
 cmd.help <- function(){
-    cat("\nVisit http://code.google.com/p/ngsplot/wiki/ProgramArguments101 for details\n")
+    cat("\nVisit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details\n")
     cat("\nUsage: replot.r command -I input.zip -O name\n")
     cat("\n  command: prof OR heatmap\n\n")
     cat("## Mandatory parameters:\n")

example/README.txt

@@ -141,7 +141,7 @@ given in "cufflinks_eg" folder.
 
 
 For more details of the usage, please visit project website:
-http://code.google.com/p/ngsplot/
+https://github.com/shenlab-sinai/ngsplot