From 970d539f1b851fae2a61267bf793b9debf10290b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 29 Jan 2018 15:46:05 +0100
Subject: [PATCH 1/4] Add possibility to color reads by sam tag

---
 public/viper/pages/inspector/inspector.html | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/public/viper/pages/inspector/inspector.html b/public/viper/pages/inspector/inspector.html
index 3000a0f..5d6a2c0 100644
--- a/public/viper/pages/inspector/inspector.html
+++ b/public/viper/pages/inspector/inspector.html
@@ -98,6 +98,17 @@ <h4>Visualization settings</h4>
             <option value="UNEXPECTED_PAIR">insert size and pair orientation</option>
             <option value="FIRST_OF_PAIR_STRAND">first-of-pair strand</option>
             <option value="READ_GROUP">read group</option>
+            <option value="TAG">tag</option>
+          </select>
+        </div>
+        <div class="form-group" ng-class="{ 'has-error': inspectorCtrl.configuration['SAM.COLOR_BY_TAG'] == null}">
+          <label>Color reads by tag:</label>
+          <input
+            type="text"
+            class="form-control"
+            ng-pattern="/^[a-zA-Z]{2}$/"
+            ng-model="inspectorCtrl.configuration['SAM.COLOR_BY_TAG']"
+            ng-change="inspectorCtrl.changeIGVSetting('SAM.COLOR_BY_TAG')">
           </select>
         </div>
         <div class="form-group">

From 74ccc03acb184f8a98238bf3a69a333cdf17a70c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marius=20W=C3=B6ste?= <mar.w@wwu.de>
Date: Tue, 30 Jan 2018 11:35:24 +0100
Subject: [PATCH 2/4] Add default value for 'color by tag'

This prevents potential configuration hashing issues.
---
 igv.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/igv.properties b/igv.properties
index 970cb82..c7d83eb 100644
--- a/igv.properties
+++ b/igv.properties
@@ -5,6 +5,7 @@ SAM.SHOW_SOFT_CLIPPED=true
 SAM.SHOW_JUNCTION_TRACK=false
 IGV.Bounds=0,0,1280,1680
 SAM.COLOR_BY=READ_STRAND
+SAM.COLOR_BY_TAG=XT
 IGV.Frame.ExtendedState=0
 SHOW_SEQUENCE_TRANSLATION=false
 SAM.DOWNSAMPLE_READS=true

From 41402744f21231740f9dc5565540f5f686a5b912 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marius=20W=C3=B6ste?= <mar.w@wwu.de>
Date: Tue, 30 Jan 2018 12:11:20 +0100
Subject: [PATCH 3/4] Allow numbers as second character in SAM tags

According to https://samtools.github.io/hts-specs/SAMv1.pdf 1.5 the second character in a tag may be a number.
.
---
 public/viper/pages/inspector/inspector.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/viper/pages/inspector/inspector.html b/public/viper/pages/inspector/inspector.html
index 5d6a2c0..5e7f6f7 100644
--- a/public/viper/pages/inspector/inspector.html
+++ b/public/viper/pages/inspector/inspector.html
@@ -106,7 +106,7 @@ <h4>Visualization settings</h4>
           <input
             type="text"
             class="form-control"
-            ng-pattern="/^[a-zA-Z]{2}$/"
+            ng-pattern="/^[A-Za-z][A-Za-z0-9]$/"
             ng-model="inspectorCtrl.configuration['SAM.COLOR_BY_TAG']"
             ng-change="inspectorCtrl.changeIGVSetting('SAM.COLOR_BY_TAG')">
           </select>

From 38e4dfd1761691eb2e3efff4c8cff997d510a9a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marius=20W=C3=B6ste?= <mar.w@wwu.de>
Date: Tue, 30 Jan 2018 13:16:19 +0100
Subject: [PATCH 4/4] Hide sam tag input when not needed

---
 public/viper/pages/inspector/inspector.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/viper/pages/inspector/inspector.html b/public/viper/pages/inspector/inspector.html
index 5e7f6f7..cda6a0d 100644
--- a/public/viper/pages/inspector/inspector.html
+++ b/public/viper/pages/inspector/inspector.html
@@ -101,7 +101,7 @@ <h4>Visualization settings</h4>
             <option value="TAG">tag</option>
           </select>
         </div>
-        <div class="form-group" ng-class="{ 'has-error': inspectorCtrl.configuration['SAM.COLOR_BY_TAG'] == null}">
+        <div ng-if="inspectorCtrl.configuration['SAM.COLOR_BY'] == 'TAG'" class="form-group" ng-class="{ 'has-error': inspectorCtrl.configuration['SAM.COLOR_BY_TAG'] == null}">
           <label>Color reads by tag:</label>
           <input
             type="text"