Improved info

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bam2tensor"
-version = "1.2"
+version = "1.3"
 description = "Bam2Tensor"
 authors = ["Nick Semenkovich <[email protected]>"]
 license = "MIT"

src/bam2tensor/__main__.py

@@ -172,7 +172,7 @@ def main(
 
         if os.path.exists(output_file) and not overwrite:
             print(
-                f"\tOutput file already exists and --overwrite not specified. Skipping {input_bam}."
+                "\tOutput file already exists and --overwrite not specified. Skipping this .bam."
             )
             skip_count += 1
             continue
@@ -204,9 +204,11 @@ def main(
         for error in errors_list:
             print(f"\t{error}")
 
-    print(f"\n{skip_count} .bam files were skipped due to existing output files.")
-
     print("\nRun complete.")
+    print(f"\n{len(bams_to_process) - skip_count} .bam files were processed.")
+    print(f"\t{skip_count} .bam files were skipped due to existing output files.")
+    print(f"\t{len(errors_list)} .bam files had errors (missing index files?).")
+    print(f"\nTotal time elapsed: {time.time() - time_start:.2f} seconds")
 
 
 if __name__ == "__main__":

src/bam2tensor/embedding.py

@@ -95,7 +95,7 @@ def __init__(
                     print("Could not load methylation embedding from cache: " + str(e))
 
         if not cache_available:
-            print("\tNo cache available, generating fresh methylation embedding.")
+            print("No cache available, generating fresh methylation embedding.")
             # Generate CpG sites if we don't have a cached embedding
             self.parse_fasta_for_cpg_sites()
 
@@ -106,7 +106,7 @@ def __init__(
                 # Save the key & expensive objects to a cache
                 self.save_embedding_cache()
         else:
-            print(f"\tLoaded methylation embedding from cache: {self.cache_file}")
+            print(f"Loaded methylation embedding from cache: {self.cache_file}")
 
         ## Generate objects for efficient lookups
         # A dict of chromosomes -> index for quick lookups (e.g. "chr1" -> 0)