feat: add vcf generate

Cargo.toml

@@ -17,6 +17,7 @@ license-file = "LICENSE"
 [features]
 fasta  = []
 fastq  = []
+vcf  = []
 derive = ["dep:biotest_derive"]
 
 [dependencies]

src/constants.rs

@@ -39,6 +39,20 @@ pub const PHRED64: [u8; 40] = gen_array::<40, 64>();
 /// Alphabets with [ \ ] ^ _ `
 pub const ALPHABETS: [u8; 58] = gen_array::<58, 65>();
 
+/// Some different possible chromosomes name
+pub const CHROMOSOMES: [&[u8]; 10] = [
+    b"chr1",
+    b"23",
+    b"93",
+    b"chrMT",
+    b"X",
+    b"NC_000015.10",
+    b"ENA|LT795502|LT795502.1",
+    b"NC_016845.1",
+    b"YAR028W",
+    b"1",
+];
+
 #[cfg(test)]
 mod tests {
     /* project use */

src/format.rs

@@ -11,4 +11,7 @@ pub mod fasta;
 #[cfg(feature = "fastq")]
 pub mod fastq;
 
+#[cfg(feature = "vcf")]
+pub mod vcf;
+
 /* projet use */

src/format/vcf.rs

@@ -0,0 +1,194 @@
+//! VCF generation
+
+/* std use */
+
+/* crates use */
+use rand::seq::SliceRandom as _;
+use rand::Rng as _;
+
+/* projet use */
+use crate::constants;
+use crate::error;
+
+/// Generate vcf header
+fn header<W>(output: &mut W) -> error::Result<()>
+where
+    W: std::io::Write,
+{
+    output.write_all(b"##fileformat=VCFv4.3\n")?;
+    for chr in constants::CHROMOSOMES {
+        output.write_all(b"##contig=<ID=")?;
+        output.write_all(chr)?;
+        output.write_all(b",length=2147483648,species=\"random\">\n")?;
+    }
+
+    output.write_all(b"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")?;
+
+    Ok(())
+}
+
+/// Generate vcf record
+fn record<W>(output: &mut W, rng: &mut rand::rngs::StdRng) -> error::Result<()>
+where
+    W: std::io::Write,
+{
+    // chromosomes
+    output.write_all(constants::CHROMOSOMES.choose(rng).unwrap())?;
+    output.write_all(b"\t")?;
+
+    // position
+    output.write_all(
+        &rng.gen_range(0..i32::MAX)
+            .to_string()
+            .bytes()
+            .collect::<Vec<u8>>(),
+    )?;
+
+    // identifiant
+    output.write_all(b"\t.\t")?;
+
+    // reference
+    output.write_all(&[*constants::NUCLEOTIDES.choose(rng).unwrap()])?;
+    output.write_all(b"\t")?;
+
+    // alternatif
+    let alt_len = rng.gen_range(1..5);
+    crate::sequence(output, rng, alt_len)?;
+    output.write_all(b"\t")?;
+
+    // quality
+    output.write_all(
+        &rng.gen_range(0..255)
+            .to_string()
+            .bytes()
+            .collect::<Vec<u8>>(),
+    )?;
+    output.write_all(b"\t")?;
+
+    // filter
+    output.write_all(b".\t")?;
+
+    // info
+    output.write_all(b"AC=")?;
+    output.write_all(
+        &rng.gen_range(0..i32::MAX)
+            .to_string()
+            .bytes()
+            .collect::<Vec<u8>>(),
+    )?;
+
+    Ok(())
+}
+
+/// Write multiple record
+pub fn records<W>(
+    output: &mut W,
+    rng: &mut rand::rngs::StdRng,
+    num_record: usize,
+) -> error::Result<()>
+where
+    W: std::io::Write,
+{
+    for _ in 0..num_record {
+        record(output, rng)?;
+        output.write_all(&[b'\n'])?;
+    }
+
+    Ok(())
+}
+
+/// Create a vcf file
+pub fn create<P>(path: P, rng: &mut rand::rngs::StdRng, num_record: usize) -> error::Result<()>
+where
+    P: std::convert::AsRef<std::path::Path>,
+{
+    let mut output = std::fs::File::create(&path)?;
+
+    header(&mut output)?;
+    records(&mut output, rng, num_record)?;
+
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    /* std use */
+    use std::io::Read as _;
+
+    /* project use */
+    use super::*;
+
+    const TRUTH: &[u8] = b"##fileformat=VCFv4.3
+##contig=<ID=chr1,length=2147483648,species=\"random\">
+##contig=<ID=23,length=2147483648,species=\"random\">
+##contig=<ID=93,length=2147483648,species=\"random\">
+##contig=<ID=chrMT,length=2147483648,species=\"random\">
+##contig=<ID=X,length=2147483648,species=\"random\">
+##contig=<ID=NC_000015.10,length=2147483648,species=\"random\">
+##contig=<ID=ENA|LT795502|LT795502.1,length=2147483648,species=\"random\">
+##contig=<ID=NC_016845.1,length=2147483648,species=\"random\">
+##contig=<ID=YAR028W,length=2147483648,species=\"random\">
+##contig=<ID=1,length=2147483648,species=\"random\">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+YAR028W	509242864	.	a	ATg	6	.	AC=730431288
+NC_016845.1	127722615	.	t	GTTA	97	.	AC=549947617
+chr1	993087666	.	a	cAcg	122	.	AC=1985475776
+chr1	223251961	.	a	cT	204	.	AC=1940638485
+23	1676586806	.	a	AG	248	.	AC=1909766224
+";
+
+    #[test]
+    fn header_() -> error::Result<()> {
+        let mut output = Vec::new();
+
+        header(&mut output)?;
+
+        assert_eq!(output, TRUTH[..628]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn record_() -> error::Result<()> {
+        let mut output = Vec::new();
+        let mut rng = crate::rand();
+
+        record(&mut output, &mut rng)?;
+
+        assert_eq!(output, TRUTH[628..670]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn records_() -> error::Result<()> {
+        let mut output = Vec::new();
+        let mut rng = crate::rand();
+
+        records(&mut output, &mut rng, 5)?;
+
+        assert_eq!(output, TRUTH[628..]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn create_() -> error::Result<()> {
+        let mut rng = crate::rand();
+
+        let temp_dir = tempfile::tempdir()?;
+        let temp_path = temp_dir.path();
+
+        let temp_file = temp_path.join("tmp.vcf");
+
+        create(&temp_file, &mut rng, 5)?;
+
+        let mut data = Vec::new();
+        let mut input = std::fs::File::open(&temp_file)?;
+        input.read_to_end(&mut data)?;
+
+        assert_eq!(data, TRUTH);
+
+        Ok(())
+    }
+}