Expand description
Automatic library-type detection.
Port of salmon’s LibraryTypeDetector
(include/.../model/LibraryTypeDetector.hpp). During the first reads of a
run, the observed LibraryFormat of each confidently mapped fragment is
tallied; once enough samples are seen, the most likely orientation and
strandedness are inferred from the count ratios using salmon’s 30%/70%
thresholds.
Structs§
- Library
Type Detector - Accumulates observed library formats and infers the most likely type.
Constants§
- DEFAULT_
SAMPLES_ NEEDED - Default number of samples to collect before guessing (matches salmon).
Functions§
- infer_
format_ from_ counts - Pure inference of the most likely library format from per-format counts
(indexed by
LibraryFormat::format_id), applying salmon’s orientation and strandedness thresholds. Order-independent — used both by the prefix-samplingLibraryTypeDetectorand by RAD auto-detection, which tallies all unique fragments rather than a thread-order-dependent prefix. Falls back to inward/unstranded when there are no usable samples.