V2.2 (#5)

-simplify config files -prevent non-zero exit code -minor algorithm improvements
PacificBiosciences · Apr 29, 2023 · 52a7f52 · 52a7f52
1 parent 775c1d1
commit 52a7f52
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diff --git a/README.md b/README.md
@@ -53,17 +53,18 @@ python setup.py install
 ## Running the program
 
 ```bash
-paraphase -b input.bam -o output_directory
+paraphase -b input.bam -o output_directory -r genome_fasta
 ```
 
 Alternatively when you have a list of bam files
 ```bash
-paraphase -l list.txt -o output_directory
+paraphase -l list.txt -o output_directory -r genome_fasta
 ```
 
 Required parameters:
 - `-b`: Input BAM file or `-l`: text file listing BAM files one per line
 - `-o`: Output directory
+- `-r`: Path to the reference genome fasta file
 
 Optional parameters:
 - `-g`: Gene(s) to analyze. All supported genes will be analyzed if not specified.

diff --git a/paraphase/__init__.py b/paraphase/__init__.py
@@ -1 +1 @@
-__version__ = "2.1.0"
+__version__ = "2.2.1"
diff --git a/paraphase/__main__.py b/paraphase/__main__.py
@@ -1,4 +1,10 @@
-from .paraphase import main
+from .paraphase import Paraphase
+
+
+def main():
+    app = Paraphase()
+    app.run()
+
 
 if __name__ == "__main__":
     main()
diff --git a/paraphase/data/cfc1/cfc1_config.yaml b/paraphase/data/cfc1/cfc1_config.yaml