sam-formatter

Convert SAM/BAM alignment files into a uniform tabular format — CSV, TSV, PSV, Parquet, or any custom delimiter — with optional SAM tags promoted to their own sorted columns.

• Reads SAM (text) and BAM (binary/BGZF) from a file or standard input.
• Auto-detects format from magic bytes (--input-format to override).
• Outputs CSV (default), TSV, PSV, Parquet, or a custom delimiter.
• Optional tags (NM, RG, MD, …) become their own columns, sorted alphabetically.
• Two-phase discover-then-stream; tag discovery is capped at min(--detect-limit, --limit) so memory stays bounded.
• Parquet output is typed: FLAG/POS/MAPQ/PNEXT/TLEN as int32, text and tags as utf8, missing tags as NULL.
• Downsample: --downsample 0.1 keeps ~10% of records (Bernoulli); --downsample 1000 keeps exactly 1000 uniformly random records (reservoir sampling). --seed makes a sample reproducible.

conda install -c conda-forge -c bioconda sam-formatter
mamba install -c conda-forge -c bioconda sam-formatter   # faster solver
pixi global install sam-formatter                         # pixi

cargo install sam-formatter

Requires Rust ≥ 1.89 (noodles).

git clone https://github.com/jiangyun-fun/sam-formatter.git
cd sam-formatter
cargo install --path .
# or: cargo build --release   # binary at target/release/sam-formatter

Prebuilt images auto-built from the Bioconda package (no Rust toolchain needed):

# Docker
docker run --rm -v "$PWD:$PWD" -w "$PWD" \
  quay.io/biocontainers/sam-formatter:1.2.0--hab7d0fd_0 sam-formatter --help
# Podman (drop-in for Docker)
podman run --rm -v "$PWD:$PWD" -w "$PWD" \
  quay.io/biocontainers/sam-formatter:1.2.0--hab7d0fd_0 sam-formatter --help

# Singularity / Apptainer
singularity exec docker://quay.io/biocontainers/sam-formatter:1.2.0--hab7d0fd_0 sam-formatter --help

See all tags at quay.io/biocontainers/sam-formatter.

sam-formatter in.sam                        # SAM file -> CSV on stdout
sam-formatter in.bam                        # BAM file -> CSV (auto-detected)
cat in.sam | sam-formatter -                # SAM from stdin
samtools view -b in.bam | sam-formatter -   # BAM from stdin

Output format:

sam-formatter in.bam -o out.tsv             # extension -> TSV
sam-formatter in.bam -o out.parquet         # Parquet
sam-formatter in.bam -f psv                 # pipe-separated
sam-formatter in.bam -f custom -d ';'       # any custom delimiter

Tags:

sam-formatter in.sam                        # NM:i:1 -> "1"        (value only)
sam-formatter in.sam --keep-tag-prefix      # NM:i:1 -> "NM:i:1"   (full tag)

Downsampling:

sam-formatter in.bam --downsample 0.1            # keep ~10% of records (Bernoulli)
sam-formatter in.bam --downsample 1000           # keep exactly 1000 random records (reservoir)
sam-formatter in.bam --downsample 1000 --seed 7  # reproducible sample

A fraction in (0, 1) keeps each record independently (≈ that share of the input); an integer ≥ 1 keeps exactly that many records via reservoir sampling (held in memory; the whole stream is read before any output). --limit caps the input before sampling.

• When piping SAM text, include the header (samtools view -h): records whose RNAME is not declared in an @SQ line are rejected. BAM carries its header internally, so no special handling is needed.
• A gzip-compressed SAM is not read directly (auto-detect misreads it as BAM, and the tool does not decompress). Decompress first: zcat in.sam.gz | sam-formatter.
• A mate reference equal to RNAME is written as = (matches samtools view).

Parsing uses noodles for both SAM and BAM via the shared sam::alignment::Record trait. Each record is serialized to a canonical SAM line with noodles' own writer and then split into columns — so CIGAR, SEQ/QUAL, and typed tag formatting are always spec-correct, identically for SAM and BAM.

Licensed under the MIT License.