From 6d015ac3c8bbcecfd9e02aa59cd79facf30617b2 Mon Sep 17 00:00:00 2001
From: Xiao Chen <chenxecho@gmail.com>
Date: Mon, 1 May 2023 12:52:48 -0700
Subject: [PATCH] fix low depth error, add version (#6)

---
 paraphase/__init__.py            |  2 +-
 paraphase/paraphase.py           | 11 +++++++++++
 paraphase/prepare_bam_and_vcf.py |  2 --
 setup.py                         |  3 ++-
 4 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/paraphase/__init__.py b/paraphase/__init__.py
index b19ee4b..ba51ced 100755
--- a/paraphase/__init__.py
+++ b/paraphase/__init__.py
@@ -1 +1 @@
-__version__ = "2.2.1"
+__version__ = "2.2.2"
diff --git a/paraphase/paraphase.py b/paraphase/paraphase.py
index c480ab2..010f950 100755
--- a/paraphase/paraphase.py
+++ b/paraphase/paraphase.py
@@ -33,6 +33,14 @@ def __init__(self):
         self.samtools = None
         self.minimap2 = None
 
+    @staticmethod
+    def get_version():
+        with open(os.path.join(os.path.dirname(__file__), "__init__.py")) as f:
+            for line in f:
+                if "version" in line:
+                    return line.split('"')[1]
+        return None
+
     def parse_configs(self, region_config=None):
         """
         Parse config files
@@ -365,6 +373,9 @@ def load_parameters(self):
             help="Optional path to minimap2",
             required=False,
         )
+        parser.add_argument(
+            "-v", "--version", action="version", version=f"{self.get_version()}"
+        )
         return parser
 
     def run(self):
diff --git a/paraphase/prepare_bam_and_vcf.py b/paraphase/prepare_bam_and_vcf.py
index 02c8975..fbbb81e 100755
--- a/paraphase/prepare_bam_and_vcf.py
+++ b/paraphase/prepare_bam_and_vcf.py
@@ -283,8 +283,6 @@ def set_parameter(self, config, tmpdir=None):
         self.bam = os.path.join(
             tmpdir, self.sample_id + f"_{self.gene}_realigned_tagged.bam"
         )
-        if os.path.exists(self.bam) is False:
-            raise Exception(f"{self.bam} does not exist. VCFs are not generated...")
         self.vcf_dir = os.path.join(self.outdir, f"{self.sample_id}_vcfs")
         if os.path.exists(self.vcf_dir) is False:
             os.makedirs(self.vcf_dir)
diff --git a/setup.py b/setup.py
index fe5a099..8f57d6b 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,5 @@
 from setuptools import setup
+import paraphase
 
 
 def readme():
@@ -8,7 +9,7 @@ def readme():
 
 setup(
     name="paraphase",
-    version="2.2.1",
+    version=paraphase.__version__,
     description="paraphase: HiFi-based caller for highly homologous genes",
     long_description=readme(),
     url="https://github.com/PacificBiosciences/paraphase",