From 3926a80dca6f181d42b900206f71d0486ef1543e Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Mon, 23 Sep 2024 16:07:29 +0200
Subject: [PATCH] Fix unstable variants in models output

---
 CHANGELOG.md                             | 7 ++++++-
 genmod/score_variants/compound_scorer.py | 2 ++
 requirements.txt                         | 1 +
 setup.py                                 | 3 ++-
 4 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 27b7d0b..d5bce0e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,11 @@ Please add a new candidate release at the top after changing the latest one. Fee
 
 Try to use the following format:
 
+## [3.8.3]
+
+- [#134](https://github.com/Clinical-Genomics/genmod/pull/134) - Fixed unstable compounds order in models output ([#133](https://github.com/Clinical-Genomics/genmod/issues/133))
+- [#134](https://github.com/Clinical-Genomics/genmod/pull/134) - Added `six` to requirements.txt and setup.py
+
 ## [3.8.0]
 - Rank score normalisation
 
@@ -22,4 +27,4 @@ Try to use the following format:
 - Adds support for escaped characters in FORMAT description header strings
 
 ### Fixed
-- Documentation about cli options `strict` and `phased`
\ No newline at end of file
+- Documentation about cli options `strict` and `phased`
diff --git a/genmod/score_variants/compound_scorer.py b/genmod/score_variants/compound_scorer.py
index a11aa71..388aad7 100755
--- a/genmod/score_variants/compound_scorer.py
+++ b/genmod/score_variants/compound_scorer.py
@@ -267,6 +267,8 @@ def run(self):
                             new_compound = "{0}>{1}".format(compound_id, compound_score)
                             scored_compound_list.append(new_compound)
 
+                        # Sort compound variants lexicographically
+                        scored_compound_list.sort()
                         new_compound_string = "{0}:{1}".format(
                             compound_family_id, '|'.join(scored_compound_list))
 
diff --git a/requirements.txt b/requirements.txt
index 3c47ac6..6028fc9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,3 +7,4 @@ configobj == 5.0.8
 intervaltree == 3.1.0
 extract_vcf == 0.5
 vcftoolbox == 1.5.1
+six == 1.16.0
diff --git a/setup.py b/setup.py
index c1fa1ba..fe9106f 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,8 @@
         'configobj >= 5.0.8',
         'intervaltree >= 3.1.0',
         'extract_vcf >= 0.5',
-        'vcftoolbox >= 1.5.1'
+        'vcftoolbox >= 1.5.1',
+        'six >= 1.16.0',
     ],
     packages=find_packages(
         exclude=('tests*', 'docs', 'examples', 'configs')