From 53591d36101163c60a53c266a9d3880600f4c99a Mon Sep 17 00:00:00 2001
From: Alex Sickler <sicklera@chop.edu>
Date: Fri, 12 Jan 2024 14:39:29 -0500
Subject: [PATCH 1/2] :heavy_plus_sign: regenerate requirements.txt

---
 requirements.txt | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 96ae92b..df12df2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1,12 @@
-samtools==1.15.1
\ No newline at end of file
+certifi==2023.11.17
+charset-normalizer==3.3.2
+idna==3.6
+numpy==1.24.4
+pandas==2.0.3
+pysam==0.22.0
+python-dateutil==2.8.2
+pytz==2023.3.post1
+requests==2.31.0
+six==1.16.0
+tzdata==2023.4
+urllib3==2.1.0

From 0821cc60272bd13186c152ced74bc99d45471ec5 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sicklera@chop.edu>
Date: Fri, 12 Jan 2024 16:10:35 -0500
Subject: [PATCH 2/2] :heavy_minus_sign: remove samtools requirement and use
 python library pysam instead

---
 .../modules/validation/check_readgroup.py     | 41 +++++++++----------
 1 file changed, 19 insertions(+), 22 deletions(-)

diff --git a/d3b_dff_cli/modules/validation/check_readgroup.py b/d3b_dff_cli/modules/validation/check_readgroup.py
index cb28c84..f80215e 100644
--- a/d3b_dff_cli/modules/validation/check_readgroup.py
+++ b/d3b_dff_cli/modules/validation/check_readgroup.py
@@ -1,45 +1,42 @@
 #!/usr/bin/env python
 import os
-import sys
-import subprocess
 import argparse
-
-def check_samtools():
-    try:
-        subprocess.run(['samtools', '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
-    except subprocess.CalledProcessError as e:
-        print("Error: 'samtools' not found. Please install samtools.")
-        sys.exit(1)
+import pysam
 
 def check_rg(file_path):
+    """Check if the BAM header contains an RG line."""
     try:
-        # Check if the BAM header contains an RG line
-        header_result = subprocess.run(['samtools', 'view', '-H', file_path], stdout=subprocess.PIPE, check=True)
-        header_lines = header_result.stdout.decode().split('\n')
-        if not any(line.startswith('@RG') for line in header_lines):
-            sample_result = subprocess.run(['samtools', 'view', file_path], stdout=subprocess.PIPE, check=True)
-            sample_lines = sample_result.stdout.decode().split('\n')[:5000]
-            if not any('RG:' in line for line in sample_lines):
-                print(f"Error: No @RG found in the header or the first 5k reads of {file_path}.")
-    except subprocess.CalledProcessError as e:
+        bam = pysam.AlignmentFile(file_path, "rb")
+        header = bam.header.to_dict()
+        if not "RG" in header:
+            # search first 5k lines, and see if any start with @RG
+            sample_lines = bam.head(5000)
+            if not any("RG:" in line.to_string() for line in sample_lines):
+                print(
+                    f"Error: No @RG found in the header or the first 5k reads of {file_path}."
+                )
+    except Exception as e:
         print(f"Error processing {file_path}: {e}")
 
+
 def main(args):
-    # Check if samtools is available before processing arguments
-    check_samtools()
     for bam_file in args.bam_files:
         # Check if bam format
         if not bam_file.endswith((".bam", ".BAM")):
             print(f"Error: Bam file {bam_file} must end with '.bam' or '.BAM'")
             continue
-        
+
         if not os.path.exists(bam_file):
             print(f"File not found: {bam_file}")
         else:
+            #deprecated_check_rg(bam_file)
             check_rg(bam_file)
 
+
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Check the presence of @RG information in the header or the first 5k reads of BAM files.")
+    parser = argparse.ArgumentParser(
+        description="Check the presence of @RG information in the header or the first 5k reads of BAM files."
+    )
     parser.add_argument("bam_files", nargs="+", help="One or more BAM files to check.")
     args = parser.parse_args()
     main(args)