Struct SamBuilder 

pub struct SamBuilder {
    pub header: Header,
    /* private fields */
}

Builder for creating test SAM/BAM records and files.

This builder simplifies test record creation by providing methods to add paired-end and single-end reads with sensible defaults. Records are accumulated internally and can be written to a file or iterated over.

Examples

use fgumi_sam::builder::{SamBuilder, Strand};

// Create a builder with defaults
let mut builder = SamBuilder::new();

// Add a mapped pair
let pair = builder.add_pair()
    .contig(0)
    .start1(100)
    .start2(200)
    .build();

// Add a fragment
let frag = builder.add_frag()
    .name("frag1")
    .bases("ACGTACGT")
    .contig(0)
    .start(150)
    .build();

// Write to a temp file
let path = builder.to_temp_file().unwrap();

Fields

header: Header

SAM header

Implementations

impl SamBuilder

pub fn new() -> SamBuilder

Creates a new builder with default settings.

Default settings:

• Read length: 100
• Base quality: 30
• Read group ID: “A”
• Sample name: “Sample”
• Reference sequences: chr1-chr22, chrX, chrY, chrM (200MB each)

pub fn with_defaults(read_length: usize, base_quality: u8) -> SamBuilder

Creates a new builder with specified read length and base quality.

Panics

Panics if DEFAULT_REFERENCE_LENGTH is zero (impossible in practice).

pub fn new_unmapped() -> SamBuilder

Creates a builder for unmapped reads (no reference sequences in header).

pub fn with_single_ref(ref_name: &str, ref_length: usize) -> SamBuilder

Creates a builder with a single reference sequence.

Panics

Panics if ref_length is zero.

pub fn records(&self) -> &[RecordBuf]

Returns a reference to the accumulated records.

pub fn len(&self) -> usize

Returns the number of accumulated records.

pub fn is_empty(&self) -> bool

Returns true if no records have been added.

pub fn clear(&mut self)

Clears all accumulated records.

pub fn iter(&self) -> impl Iterator<Item = &RecordBuf>

Returns an iterator over the accumulated records.

pub fn push_record(&mut self, record: RecordBuf)

Pushes a raw record to the collection.

This is useful when you need to add pre-built records to the collection.

pub fn add_pair(&mut self) -> PairBuilder<'_>

Starts building a paired-end read pair.

Returns a PairBuilder that can be configured and then built. The resulting records are added to this builder and also returned.

pub fn add_frag(&mut self) -> FragBuilder<'_>

Starts building a single-end (fragment) read.

Returns a FragBuilder that can be configured and then built. The resulting record is added to this builder and also returned.

pub fn write_bam(&self, path: &Path) -> Result<(), Error>

Writes accumulated records to a BAM file.

Errors

Returns an error if the file cannot be created or written.

pub fn write_sam(&self, path: &Path) -> Result<(), Error>

Writes accumulated records to a SAM file.

Errors

Returns an error if the file cannot be created or written.

pub fn to_temp_file(&self) -> Result<NamedTempFile, Error>

Writes to a temporary BAM file and returns the path.

Errors

Returns an error if the temporary file cannot be created or written.

impl SamBuilder

pub fn new_mapped() -> SamBuilder

Creates a new builder for mapped BAM files with a single reference.

Creates a builder with “chr1” as the reference name and REFERENCE_LENGTH as length.

pub fn add_pair_with_attrs( &mut self, name: &str, start1: Option<usize>, start2: Option<usize>, strand1: bool, strand2: bool, attrs: &HashMap<&str, Value>, )

Adds a pair using positional arguments.

A convenience method for adding pairs with common parameters.

Arguments

• name - Read name
• start1 - Start position for R1 (None = unmapped)
• start2 - Start position for R2 (None = unmapped)
• strand1 - true = Plus, false = Minus for R1
• strand2 - true = Plus, false = Minus for R2
• attrs - Attributes to add to both reads

pub fn add_frag_with_attrs( &mut self, name: &str, start: Option<usize>, strand: bool, attrs: &HashMap<&str, Value>, )

Adds a fragment using positional arguments.

A convenience method for adding fragments with common parameters.

Arguments

• name - Read name
• start - Start position (None = unmapped)
• strand - true = Plus, false = Minus
• attrs - Attributes to add

pub fn write(&self, path: &Path) -> Result<(), Error>

Writes accumulated records to a BAM file.

Alias for write_bam.

Errors

Returns an error if the BAM file cannot be created or written to.

Trait Implementations

impl Debug for SamBuilder

fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

impl Default for SamBuilder

fn default() -> SamBuilder

Returns the “default value” for a type.