From 762b8ac7c6791240265a986e2f3276a9cd8ceb3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Tue, 26 Nov 2024 13:58:00 +0100 Subject: [PATCH] imporve docs / and READMe --- README.md | 1 + src/sr2silo/process.py | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f3c189c..34ac11d 100644 --- a/README.md +++ b/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. diff --git a/src/sr2silo/process.py b/src/sr2silo/process.py index 05d40ed..b244bab 100644 --- a/src/sr2silo/process.py +++ b/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,