Class SequenceStatsCalculator

High-performance sequence statistics calculator with streaming support

Calculates comprehensive statistics from sequences while maintaining constant memory usage through streaming computation where possible.

Example

// Basic statistics
const calculator = new SequenceStatsCalculator();
const stats = await calculator.calculateStats(sequences);
console.log(`N50: ${stats.n50}, GC: ${stats.gcContent}%`);

// Detailed statistics with quality
const detailedStats = await calculator.calculateStats(sequences, {
  detailed: true,
  includeQuality: true,
  includeComposition: true
});

// Tabular output for command-line
const tableStats = await calculator.calculateStats(sequences, {
  tabular: true,
  fileName: 'genome.fasta'
});

Index

Constructors

constructor

Methods

calculateStats calculateNX calculateQualityStats

Constructors

constructor

new SequenceStatsCalculator(): SequenceStatsCalculator
Returns SequenceStatsCalculator

Methods

calculateStats

calculateStats(
sequences: AsyncIterable<AbstractSequence | FASTXSequence>,
options?: StatsOptions,
): Promise<SequenceStats>
Calculate comprehensive sequence statistics

Processes sequences through a single pass, computing all requested statistics while maintaining memory efficiency.
Parameters
- sequences: AsyncIterable<AbstractSequence | FASTXSequence>
  Input sequences to analyze
- options: StatsOptions = {}
  Configuration options for statistics
Returns Promise<SequenceStats>
Comprehensive statistics result
Example
```
const stats = await calculator.calculateStats(sequences, {
  detailed: true,
  includeComposition: true
});
```
- Defined in src/operations/stats.ts:258

calculateNX

calculateNX(lengths: number[], percentile: number): number
Calculate N50, N90, and other percentile metrics

N50 is the sequence length where 50% of the total bases are in sequences of this length or longer. This is a key metric for genome assembly quality assessment.
Parameters
- lengths: number[]
  Array of sequence lengths (will be sorted)
- percentile: number
  Target percentile (50 for N50, 90 for N90)
Returns number
The NX value
Example
```
const lengths = [100, 200, 300, 400, 500];
const n50 = calculator.calculateNX(lengths, 50);
const n90 = calculator.calculateNX(lengths, 90);
```
- Defined in src/operations/stats.ts:319

calculateQualityStats

calculateQualityStats(
    qualities: string[],
    encoding: QualityEncoding,
): {
    mean: number;
    min: number;
    max: number;
    q20Percentage: number;
    q30Percentage: number;
}
Calculate quality statistics for FASTQ sequences

Computes mean, min, max, and percentile-based quality metrics from quality strings using the appropriate encoding.
Parameters
- qualities: string[]
  Array of quality strings
- encoding: QualityEncoding
  Quality encoding system
Returns {
    mean: number;
    min: number;
    max: number;
    q20Percentage: number;
    q30Percentage: number;
}
Quality statistics
- Defined in src/operations/stats.ts:354

Class SequenceStatsCalculator

Example

Index

Constructors

Methods

Constructors

constructor

Returns SequenceStatsCalculator

Methods

calculateStats

Parameters

Returns Promise<SequenceStats>

Example

calculateNX

Parameters

Returns number

Example

calculateQualityStats

Parameters

Returns {
    mean: number;
    min: number;
    max: number;
    q20Percentage: number;
    q30Percentage: number;
}

Settings

On This Page

Class SequenceStatsCalculator

Example

Index

Constructors

Methods

Constructors

constructor

Returns SequenceStatsCalculator

Methods

calculateStats

Parameters

Returns Promise<SequenceStats>

Example

calculateNX

Parameters

Returns number

Example

calculateQualityStats

Parameters

Returns { mean: number; min: number; max: number; q20Percentage: number; q30Percentage: number;}

Settings

On This Page

Returns {
mean: number;
min: number;
max: number;
q20Percentage: number;
q30Percentage: number;
}