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Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Read PAF mappings as ggchord links

On this page

• Usage
• Arguments
• Value
• Details
• See also
• Examples

Converts zero-based half-open PAF query/target intervals to one-based inclusive endpoints. Query endpoints increase; target endpoints decrease for relative strand "-". This display convention preserves relative orientation and does not infer a biological strand for either sequence.

Usage

Code

read_paf(file = NULL, files = NULL, source_file = FALSE)

Arguments

file

Optional path vector or glob patterns; read before files.

files

Optional paths or wildcard patterns for multiple PAF files.

source_file

Logical. Add a .source_file column, default FALSE.

Value

A link data frame with canonical endpoints, qlen, slen, nmatch, length, pident, mapq, relative orientation, original zero-based coordinates, tags and .source_line. The ggchord_import attribute records input/output coordinate conventions and files.

Details

length is the reported alignment block length, including gaps, and pident is 100 * nmatch / length using the reported PAF fields. Both counts may be approximate when the producer did not compute an alignment. The importer does not recompute an alignment, validate a CIGAR, or claim exact base identity. pident_basis records this ratio's provenance. Mapping quality 255 means unavailable: mapq becomes NA, while source_mapq retains the original value. Optional typed tags are retained verbatim in the tags list-column, including unknown tags and their order.

See also

https://github.com/lh3/miniasm/blob/master/PAF.md

ggchord_data_contract

Examples

Code

if (FALSE) { # \dontrun{
library(dplyr)
# Requires the source checkout or tutorial input bundle.
links <- read_paf("examples/format-inputs/emales-pair.paf")
links |>
  select(qaccver, saccver, qstart, qend, sstart, send)
} # }