libqcpp API

Contents

• libqcpp API
  • Overview
  • Streams
  • Processors
    • AdaptorTrimPE
    • WindowedQCTrim
    • PerBaseQuality
    • ReadLenFilter
    • ReadLenCounter
    • ReadTruncator

Overview

libqcpp’s API is built around two concepts: Stream and Processors.

Streams

ReadStreams are streams of sequence reads. These streams parse reads from or write reads to a file or stream. ReadInputStream and ReadOutputStream do so without any manipulation. A ProcessedReadStream processes reads using a pipeline of processors. ThreadedQCProcessor is a high-level, multi-threaded read processor that reads from and writes to files directly. Streams can report, as member variables or as a YAML report, statistics on reads that have been parsed or written.

Processors

Processors mutate or calculate statistics on a read or read pair. They may also report statistics on all reads they have processed in their lifetime, as member variables or as YAML reports.

The following processors are implemented (shown with constructor arguments).

AdaptorTrimPE

AdaptorTrimPE(const std::string &name, int min_overlap=10,
              const QualityEncoding &encoding=SangerEncoding);

Aligns a read pair to each other, and detect either adaptor read-through, or read overlap. Operates only on paired reads. Yields single ended reads if the read pair is either shorter than the read length (thus each read contains adaptor sequence) or the read ends overlap.

WindowedQCTrim

WindowedQualTrim(const std::string &name, int8_t min_quality,
                 size_t min_length, size_t window_size=0,
                 const QualityEncoding &encoding=SangerEncoding);

Uses a sliding-window based approach to trim reads at the point where base quality decreases below a threshold. Reads are trimmed at the first position at which a window’s mean base quality is below min_quality. The 5’ end of a read is also trimmed. Reads less than min_length bases long are removed from the stream. The window size may be set using window_size; a window_size value of 0 causes the window length to be 10% of the read length.

PerBaseQuality

PerBaseQuality(const std::string &name,
               const QualityEncoding &encoding=SangerEncoding);

Records statistics on per-cycle quality across all read sets, reporting the distribution of base quality scores for each cycle.

ReadLenFilter

ReadLenFilter(const std::string &name,
              size_t             threshold = 1,
              const QualityEncoding &encoding=SangerEncoding);

Filters reads less than threshold bases out of a stream.

ReadLenCounter

ReadLenCounter(const std::string &name,
               const QualityEncoding &encoding=SangerEncoding);

Counts the length distribution of all reads.

ReadTruncator

ReadTruncator(const std::string &name,
              size_t threshold=64,
              const QualityEncoding &encoding=SangerEncoding);

Truncates reads to threshold bases long, and removes reads from the stream less than threshold bases long.