From d35df727477f4469242548ac5dafaf945c77a008 Mon Sep 17 00:00:00 2001
From: ljwharbers <l.j.w.harbers@gmail.com>
Date: Wed, 16 Oct 2024 15:02:17 +0200
Subject: [PATCH] added --version capability and bumped version

---
 src/flexi_formatter/__init__.py               |  2 +-
 .../reformat_flexiplex_tags.py                | 39 ++++++++++++-------
 2 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/src/flexi_formatter/__init__.py b/src/flexi_formatter/__init__.py
index e82265b..06f3834 100644
--- a/src/flexi_formatter/__init__.py
+++ b/src/flexi_formatter/__init__.py
@@ -1,3 +1,3 @@
 """Tool to reformat flexiplex tags in a bam file"""
 
-__version__ = "0.0.4"
\ No newline at end of file
+__version__ = "1.0.0"
\ No newline at end of file
diff --git a/src/flexi_formatter/reformat_flexiplex_tags.py b/src/flexi_formatter/reformat_flexiplex_tags.py
index 7339476..f376a4f 100755
--- a/src/flexi_formatter/reformat_flexiplex_tags.py
+++ b/src/flexi_formatter/reformat_flexiplex_tags.py
@@ -2,25 +2,38 @@
 import sys
 import typer
 import simplesam
+from flexi_formatter import __version__ 
 
 app = typer.Typer()
 
 @app.command()
 def main(infile: str):
-  with simplesam.Reader(open(infile)) as in_bam:
-    with simplesam.Writer(sys.stdout, in_bam.header) as out_sam:
-      for read in in_bam:
-        # Get header name and split by "_#"
-        bc_umi = read.qname.split("#")[0]
-        bc = bc_umi.split("_")[0]
-        read.tags['CB'] = bc
+    with simplesam.Reader(open(infile)) as in_bam:
+        with simplesam.Writer(sys.stdout, in_bam.header) as out_sam:
+            for read in in_bam:
+                # Get header name and split by "_#"
+                bc_umi = read.qname.split("#")[0]
+                bc = bc_umi.split("_")[0]
+                read.tags['CB'] = bc
 
-        if len(bc_umi.split("_")) > 1:
-          umi = bc_umi.split("_")[1]
-          read.tags['UR'] = umi
+                if len(bc_umi.split("_")) > 1:
+                    umi = bc_umi.split("_")[1]
+                    read.tags['UR'] = umi
 
-        # Write new reads
-        out_sam.write(read)
+                # Write new reads
+                out_sam.write(read)
+
+@app.callback()
+def callback():
+    """
+    A simple tool for processing BAM/SAM files.
+    """
+    pass
+
+@app.command()
+def version():
+    """Prints the version of the tool."""
+    typer.echo(f"flexi_formatter version: {__version__}")
 
 if __name__ == "__main__":
-  app()
+    app()
\ No newline at end of file