From 68acbd1bae99eef79602e73d1c58011538cbea79 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 13 Dec 2019 15:56:31 +0100
Subject: [PATCH 1/2] bash script to update the README

---
 README.md                      |  6 ++++--
 pygenometracks/updateREADME.sh | 15 +++++++++++++++
 2 files changed, 19 insertions(+), 2 deletions(-)
 create mode 100644 pygenometracks/updateREADME.sh

diff --git a/README.md b/README.md
index caec1db8..382a86b2 100644
--- a/README.md
+++ b/README.md
@@ -444,6 +444,7 @@ Here is a table to summarize which are the parameters that can be use for each o
 Empty means this parameter is not used.
 not set means that by default the parameter is commented.
 
+<!--- Start of default table -->
 parameter | x-axis | epilogos | links | domains | bed | narrow_peak | bigwig | bedgraph | bedgraph_matrix | hlines | hic_matrix
 -- | - | - | - | - | - | - | - | - | - | - | -
 where | bottom |  |  |  |  |  |  |  |  |  | 
@@ -490,12 +491,12 @@ show_masked_bins |  |  |  |  |  |  |  |  |  |  | false
 scale_factor |  |  |  |  |  |  |  |  |  |  | 1
 transform |  |  |  |  |  |  |  |  |  |  | no
 colormap |  |  |  |  |  |  |  |  |  |  | RdYlBu_r
-
+<!--- End of default table -->
 
 Some parameters can take only discrete values.
 
 They are summarized here:
-
+<!--- Start of possible table -->
 - **where**:
   - for *x-axis*: top, bottom
 - **orientation**:
@@ -542,6 +543,7 @@ They are summarized here:
   - for *bigwig, bedgraph*: true, false
 - **arrowhead_included**:
   - for *bed*: true, false
+<!--- End of possible table -->
 
 Adding new tracks
 -----------------
diff --git a/pygenometracks/updateREADME.sh b/pygenometracks/updateREADME.sh
new file mode 100644
index 00000000..f95ba452
--- /dev/null
+++ b/pygenometracks/updateREADME.sh
@@ -0,0 +1,15 @@
+# This bash script can be used to regenerate the README when parameters changed in tracksclasses.
+
+# Firts run the python script getAllDefaultsAndPossible.py
+python pygenometracks/getAllDefaultsAndPossible.py 
+
+# This generates 2 tables to include in the README
+# First include the first one: docs/content/all_default_properties.txt
+awk 'NR==1,/<!--- Start of default table -->/' README.md > newREADME.md
+cat docs/content/all_default_properties.txt >> newREADME.md
+awk '/<!--- End of default table -->/{toprint = 1}toprint == 1{print}' README.md >> newREADME.md
+# Then include the second one: docs/content/all_possible_properties.txt
+awk 'NR==1,/<!--- Start of possible table -->/' newREADME.md > README.md
+cat docs/content/all_possible_properties.txt >> README.md
+awk '/<!--- End of possible table -->/{toprint = 1}toprint == 1{print}' newREADME.md >> README.md
+rm newREADME.md
\ No newline at end of file

From a67407ffe389ac23c1e22003d5c86a33dbe7c6a1 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 13 Dec 2019 16:04:34 +0100
Subject: [PATCH 2/2] added a newline at the end of the file

---
 pygenometracks/updateREADME.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygenometracks/updateREADME.sh b/pygenometracks/updateREADME.sh
index f95ba452..1c7df3b8 100644
--- a/pygenometracks/updateREADME.sh
+++ b/pygenometracks/updateREADME.sh
@@ -12,4 +12,4 @@ awk '/<!--- End of default table -->/{toprint = 1}toprint == 1{print}' README.md
 awk 'NR==1,/<!--- Start of possible table -->/' newREADME.md > README.md
 cat docs/content/all_possible_properties.txt >> README.md
 awk '/<!--- End of possible table -->/{toprint = 1}toprint == 1{print}' newREADME.md >> README.md
-rm newREADME.md
\ No newline at end of file
+rm newREADME.md