fgumi SIMD FASTQ

https://docs.rs/fgumi_simd_fastq
Admin
fgumi SIMD FASTQ is a high-performance Rust crate for SIMD-accelerated FASTQ parsing using...
Tokens:858
Snippets:8
Trust Score:9.1
Update:5 months ago
Show doc for...
Tokens:
Raw
### Parse FASTQ Records and Find Offsets

Source: https://docs.rs/fgumi_simd_fastq

Demonstrates how to find record boundary offsets and parse FASTQ records from a byte buffer using the `find_record_offsets` and `parse_records` functions. Ensure the input is a valid FASTQ byte slice.

```rust
use fgumi_simd_fastq::{find_record_offsets, parse_records};

let fastq = b"@r1\nACGT\n+\nIIII\n@r2\nTTTT\n+\nJJJJ\n";
let offsets = find_record_offsets(fastq);
assert_eq!(offsets, vec![0, 16, 32]);

let records: Vec<_> = parse_records(fastq).collect();
assert_eq!(records.len(), 2);
assert_eq!(records[0].name, b"r1");
assert_eq!(records[0].sequence, b"ACGT");
```

--------------------------------

### lex_block_full

Source: https://docs.rs/fgumi_simd_fastq

Lexes a 64-byte block of FASTQ data, producing a bitmask for newline characters, an ACGT bitmask, and a 2-bit encoding. This is a low-level function used internally for SIMD processing.

```APIDOC
## lex_block_full

### Description
Lex a 64-byte block, producing newline bitmask, ACGT bitmask, and 2-bit encoding.

### Function Signature
`fn lex_block_full(block: &[u8; 64]) -> (FastqBitmask, u64, u64)`

### Parameters
- **block** (`&[u8; 64]`) - A 64-byte array representing a block of FASTQ data.

### Returns
- `(FastqBitmask, u64, u64)` - A tuple containing the newline bitmask, ACGT bitmask, and 2-bit encoding.
```

--------------------------------

### parse_records

Source: https://docs.rs/fgumi_simd_fastq

Provides an iterator over zero-copy FASTQ records parsed directly from a byte buffer. Each record is represented as a borrowed struct, avoiding unnecessary data copying.

```APIDOC
## parse_records

### Description
Iterator over zero-copy FASTQ records parsed from a byte buffer.

### Function Signature
`fn parse_records(fastq: &[u8]) -> impl Iterator<Item = FastqRecord>`

### Parameters
- **fastq** (`&[u8]`) - The byte slice containing FASTQ formatted data.

### Returns
- `impl Iterator<Item = FastqRecord>` - An iterator yielding `FastqRecord` structs.
```

--------------------------------

### find_record_offsets

Source: https://docs.rs/fgumi_simd_fastq

Finds the byte offsets of FASTQ record boundaries within a given byte buffer. This function is useful for pre-calculating record locations before parsing.

```APIDOC
## find_record_offsets

### Description
Find FASTQ record boundary offsets in a byte buffer.

### Function Signature
`fn find_record_offsets(fastq: &[u8]) -> Vec<usize>`

### Parameters
- **fastq** (`&[u8]`) - The byte slice containing FASTQ formatted data.

### Returns
- `Vec<usize>` - A vector of byte offsets indicating the start of each FASTQ record.
```
Tokens:
Raw