From 66f976aebd3e6603522b9c61215f12a3057f470e Mon Sep 17 00:00:00 2001
From: Bryce Turner <40504111+bryce-turner@users.noreply.github.com>
Date: Fri, 4 Sep 2020 13:54:09 -0700
Subject: [PATCH 1/7] Update pipeline.yaml

---
 pipeline.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline.yaml b/pipeline.yaml
index 4c67d423..7017c0e1 100644
--- a/pipeline.yaml
+++ b/pipeline.yaml
@@ -2,7 +2,7 @@ __pipeline__:
   name: phoenix
   main: main.jst
   description: Human GRCh38 genomics suite
-  version: development
+  version: v1.0.2
 constants:
   tools:
     bedtools:

From f26d5b6a9066a5872bbf52994963f05fffc29011 Mon Sep 17 00:00:00 2001
From: Bryce Turner <40504111+bryce-turner@users.noreply.github.com>
Date: Thu, 4 Feb 2021 11:25:00 -0700
Subject: [PATCH 2/7] Increment pipeline version

---
 pipeline.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline.yaml b/pipeline.yaml
index 8b527a01..f4c62ed2 100644
--- a/pipeline.yaml
+++ b/pipeline.yaml
@@ -2,7 +2,7 @@ __pipeline__:
   name: phoenix
   main: main.jst
   description: Human GRCh38 genomics suite
-  version: v1.0.2
+  version: v1.1.0
 constants:
   tools:
     bedtools:

From 30d834db10649c504395bdb4801344ca50522647 Mon Sep 17 00:00:00 2001
From: Bryce Turner <40504111+bryce-turner@users.noreply.github.com>
Date: Fri, 12 Mar 2021 14:54:51 -0700
Subject: [PATCH 3/7] Pipeline version bump for v1.1.1

---
 pipeline.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline.yaml b/pipeline.yaml
index bbddee53..527dc56c 100644
--- a/pipeline.yaml
+++ b/pipeline.yaml
@@ -2,7 +2,7 @@ __pipeline__:
   name: phoenix
   main: main.jst
   description: Human GRCh38 genomics suite
-  version: v1.1.0
+  version: v1.1.1
 constants:
   tools:
     bedtools:

From ace7746dca4c3d503171740099f2162fdf0c2757 Mon Sep 17 00:00:00 2001
From: Bryce Turner <40504111+bryce-turner@users.noreply.github.com>
Date: Wed, 17 Mar 2021 12:20:06 -0700
Subject: [PATCH 4/7] Update pipeline.yaml

---
 pipeline.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline.yaml b/pipeline.yaml
index 4858afde..9e250a54 100644
--- a/pipeline.yaml
+++ b/pipeline.yaml
@@ -2,7 +2,7 @@ __pipeline__:
   name: phoenix
   main: main.jst
   description: Human GRCh38 genomics suite
-  version: v1.1.1
+  version: v1.1.2
 constants:
   tools:
     bedtools:

From 2834c7b8f046c4fd28b47d1b0962fdf7e1a07621 Mon Sep 17 00:00:00 2001
From: Bryce Turner <40504111+bryce-turner@users.noreply.github.com>
Date: Wed, 4 Aug 2021 10:32:54 -0700
Subject: [PATCH 5/7] Update pipeline.yaml

---
 pipeline.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline.yaml b/pipeline.yaml
index a968a5d3..867d2b75 100644
--- a/pipeline.yaml
+++ b/pipeline.yaml
@@ -2,7 +2,7 @@ __pipeline__:
   name: phoenix
   main: main.jst
   description: Human GRCh38 genomics suite
-  version: v1.1.2
+  version: v1.2
 constants:
   tools:
     bedtools:

From 0fc0c0638b63f5cc4519bc0e1d5cbb4ae12b5a8e Mon Sep 17 00:00:00 2001
From: Bryce Turner <40504111+bryce-turner@users.noreply.github.com>
Date: Wed, 4 Aug 2021 10:36:00 -0700
Subject: [PATCH 6/7] Update pipeline.yaml

---
 pipeline.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline.yaml b/pipeline.yaml
index 867d2b75..5cc12ec4 100644
--- a/pipeline.yaml
+++ b/pipeline.yaml
@@ -2,7 +2,7 @@ __pipeline__:
   name: phoenix
   main: main.jst
   description: Human GRCh38 genomics suite
-  version: v1.2
+  version: v1.2.0
 constants:
   tools:
     bedtools:

From 854dceda06f75b15463564d2d6befbc6128354b8 Mon Sep 17 00:00:00 2001
From: Tyler Izatt <tizatt@tgen.org>
Date: Mon, 26 Sep 2022 10:04:31 -0700
Subject: [PATCH 7/7] Update annotSeg_7102f1c.pl

AnnotSeg creates a window from which genes are selected from the ensembl gtf.  This window was found to be too large and is annotating beyond the actual region of genes.  Because it was doing a division/multiplication before a subtraction - this caused windows to be thousands of bp larger than what they actually should be.  This fix takes care of making the window size more accurate by doing the subtraction/addition before multiplication/division.
---
 required_scripts/annotSeg_7102f1c.pl | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/required_scripts/annotSeg_7102f1c.pl b/required_scripts/annotSeg_7102f1c.pl
index 139ff4bd..b386cdb9 100755
--- a/required_scripts/annotSeg_7102f1c.pl
+++ b/required_scripts/annotSeg_7102f1c.pl
@@ -64,10 +64,13 @@
 
 my %gene;
 foreach my $k (keys %geneA){
-	$st=int($loc{$k}/100);
-	$en=int($loc2{$k}/100);
+        $st1=int($loc{$k}-100);
+	$st=int($st1/100);
+	$en1=int($loc{$k}+100);
+	$en=int($en1/100);
+	
 	if ($st>$en) {$t=$en;$en=$st;$st=$t;}
-        for ($i=$st-100;$i<=$en+100;++$i*100) {
+        for ($i=$st;$i<=$en;++$i*100) {
 		if ($chr{$k} eq "X") {$chr{$k}=23;}
 		if ($chr{$k} eq "Y") {$chr{$k}=24;}
                 if (exists($gene{"$chr{$k}_$i"})) {