From 31513da3846b187b3d7f96ad14f3c71e1177b0d3 Mon Sep 17 00:00:00 2001
From: Muhammed Hasan Celik <muhammedhasancelik@gmail.com>
Date: Tue, 23 May 2023 14:09:05 -0700
Subject: [PATCH] Version 2.4 (#67)
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* kipoiseq version and use_strand

* Bump version: 2.3.0 → 2.4.0

* cyvcf2 version

* pyranges version
---
 mmsplice/__init__.py        | 2 +-
 mmsplice/exon_dataloader.py | 2 +-
 setup.cfg                   | 2 +-
 setup.py                    | 7 ++++---
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/mmsplice/__init__.py b/mmsplice/__init__.py
index ca33a51..0dcd0eb 100644
--- a/mmsplice/__init__.py
+++ b/mmsplice/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Jun Cheng & M.Hasan Celik"""
 __email__ = 'chengju@in.tum.de'
-__version__ = '2.3.0'
+__version__ = '2.4.0'
 
 from tensorflow.keras.models import load_model
 from mmsplice.mmsplice import MMSplice, \
diff --git a/mmsplice/exon_dataloader.py b/mmsplice/exon_dataloader.py
index a5b7ed8..0ece9e8 100644
--- a/mmsplice/exon_dataloader.py
+++ b/mmsplice/exon_dataloader.py
@@ -235,7 +235,7 @@ def _next(self, exon, variant, overhang=None, mask_module=None):
         inputs = {
             'seq': self.fasta.extract(Interval(
                 exon.chrom, exon.start - overhang[0],
-                exon.end + overhang[1], strand=exon.strand)).upper(),
+                exon.end + overhang[1], strand=exon.strand), use_strand=True).upper(),
             'mut_seq': self.vseq_extractor.extract(
                 exon, [variant], overhang=overhang).upper()
         }
diff --git a/setup.cfg b/setup.cfg
index 5246ec7..bdc3826 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.3.0
+current_version = 2.4.0
 commit = True
 tag = True
 
diff --git a/setup.py b/setup.py
index a1cd8b9..01f5723 100644
--- a/setup.py
+++ b/setup.py
@@ -13,7 +13,7 @@
 
 requirements = [
     'setuptools',
-    'kipoiseq>=0.7,<0.8',
+    'kipoiseq',
     'cyvcf2',
     'tensorflow',
     'scipy',
@@ -21,7 +21,8 @@
     'pyfaidx',
     'tqdm',
     'click',
-    'pyranges>=0.0.71'
+    'cyvcf2<=0.30.15',
+    'pyranges>=0.0.71,<0.0.126',
 ]
 
 setup_requirements = ['pytest-runner', ]
@@ -57,6 +58,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/gagneurlab/mmsplice',
-    version='2.3.0',
+    version='2.4.0',
     zip_safe=False
 )