imporve docs / and READMe

README.md

@@ -26,6 +26,7 @@ The V-Pipe Docker is designed to process a single `.bam` file and upload the res
 
 ## Project Organization
 
+- `silo-input-transformer`: Is a rust based utility to handle the `fasta` to `ndjson` transformation and is here imported as a git submodule.
 - `.github/workflows`: Contains GitHub Actions used for building, testing, and publishing.
 install, and whether or not to mount the project directory into the container.
 - `.vscode/settings.json`: Contains VSCode settings specific to the project, such as the Python interpreter to use and the maximum line length for auto-formatting.

src/sr2silo/process.py

@@ -30,7 +30,8 @@ def pair_normalize_reads(
     sam_data: str, output_fasta: Path, output_insertions: Path
 ) -> None:
     """
-    Pair and normalize all reads in a SAM file.
+    Pair and normalize (to clear text sequence using CIGAR)
+    all reads in a SAM file output FASTA and insertions files.
 
     Note that the input SAM file must be read in
     its entirety before calling this function,