From 76329c42e0f9351cf77278203146f14836d59d63 Mon Sep 17 00:00:00 2001
From: David K Jackson <david.jackson@sanger.ac.uk>
Date: Fri, 6 Jun 2014 14:05:35 +0100
Subject: [PATCH] Use bin and data directory heirarchy

---
 README.vtfp                                    | 8 ++++----
 viv.pl => bin/viv.pl                           | 0
 vtfp.pl => bin/vtfp.pl                         | 0
 {examples => data}/tophat2_sample_template.vtf | 0
 examples/README.examples                       | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)
 rename viv.pl => bin/viv.pl (100%)
 rename vtfp.pl => bin/vtfp.pl (100%)
 rename {examples => data}/tophat2_sample_template.vtf (100%)

diff --git a/README.vtfp b/README.vtfp
index 058dd3437..646d9f7c5 100644
--- a/README.vtfp
+++ b/README.vtfp
@@ -58,14 +58,14 @@ vtfp.pl
 
      kl2@sf2-farm-srv1:~/projects/viv$ grep -v "^#" examples/example_06.vtf | tr -d "\n\t" > example_06_vtf.json
 
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -q example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -q example_06_vtf.json
      KeyID	Req	Id	RawAttrib
      greetings_file	required	greetings_file	name
      intercept_file	not_required	intercept_file	name
 
   Preprocessing this, specifying only the required KeyID "greetings_file" gives:
 
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt example_06_vtf.json
 
      {
      'nodes' => [
@@ -112,9 +112,9 @@ vtfp.pl
 
   Preprocessing this, both substitutable parameters gives:
 
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt -keys intercept_file -vals intercept.txt example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -keys greetings_file -vals Hello.txt -keys intercept_file -vals intercept.txt example_06_vtf.json
   or:
-     kl2@sf2-farm-srv1:~/projects/viv$ vtfp.pl -l ex06.log -keys greetings_file,intercept_file -vals Hello.txt,intercept.txt example_06_vtf.json
+     kl2@sf2-farm-srv1:~/projects/viv$ bin/vtfp.pl -l ex06.log -keys greetings_file,intercept_file -vals Hello.txt,intercept.txt example_06_vtf.json
 
      {
      'nodes' => [
diff --git a/viv.pl b/bin/viv.pl
similarity index 100%
rename from viv.pl
rename to bin/viv.pl
diff --git a/vtfp.pl b/bin/vtfp.pl
similarity index 100%
rename from vtfp.pl
rename to bin/vtfp.pl
diff --git a/examples/tophat2_sample_template.vtf b/data/tophat2_sample_template.vtf
similarity index 100%
rename from examples/tophat2_sample_template.vtf
rename to data/tophat2_sample_template.vtf
diff --git a/examples/README.examples b/examples/README.examples
index f264bca13..677bce58a 100644
--- a/examples/README.examples
+++ b/examples/README.examples
@@ -7,6 +7,6 @@ For example:
   grep -v "^#" example_01.cfg | tr -d "\n\t" > example_01_cfg.json
 
 You can then use the viv script with this JSON file (if you are working from the examples directory):
-  ../viv.pl -s -x -v 3 -o example_01.log example_01_cfg.json
+  ../bin/viv.pl -s -x -v 3 -o example_01.log example_01_cfg.json
  
 The resulting log file is verbose - you may want to reduce the verbosity level (the value supplied to the -v flag).