Command line arguments

The table below show all arguments that are available in the reformat module.

Long flag	Short flag	Type	Default	Description
--help	-h	Flag	-	Print help message explaining all flags. -h shows a more compact version than --help

Required Input/Output

Long flag	Short flag	Type	Default	Description
--alignment <alignment>	-a <alignment>	Path(file)	-	Path to .parquet or .jsonl file produced by fishnet align
--out <out>	-o <out>	Path (file)	-	Output path. Extension determines format (.parquet or .tsv)

Pod5 Input

Long flag	Short flag	Type	Default	Description
--pod5 <pod5>...	-p <pod5>...	Path(s) (file or directory)	-	POD5 input(s). Required if alignment file lacks raw signal. Multiple allowed
--rna	-	Flag	-	Set if POD5 file(s) are provided and the contained reads are direct RNA (reverse signal)

Data filtering

One filtering flag is required.

Long flag	Short flag	Type	Default	Description
--ref-regions <ref-regions>...	-r <ref-regions>...	String(s)	-	Filter input data for one or more reference region(s). Each must be in the format <REF-NAME>:<REF-START>-<REF-END> (Start and end are 1-based coordinates and inclusive). Multiple can be provided space-separated
--bed-file <bed-file>	-R <bed-file>	Path (file)	-	Filter input data for reference regions from bed file. Must follow bed-style coordinate conventions (0-based, start inclusive, end exclusive)
--positions-of-interest <poi>...	-P <poi>...	String(s)	-	Filter input data for one or more positions of interest. Each must be in the format <REF-NAME>:<REF-SITE>-<HALF-SIZE>, where determines the number of bases up- and downstream from the site that are of interest. Site coordinate is 1-based
--motifs <motif>...	-m <motif>...	String(s)	-	Filter for motif sequence(s). Sequences must contain only 'A', 'C', 'G' and 'T'/'U'. Multiple can be provided space-separated
--motifs-file <motifs-file>	-M <motifs-file>	Path (file)	-	Filter input data for reference regions from a FASTA file. Each motif must be a separate entry. Sequences must contain only 'A', 'C', 'G' and 'T'/'U'

Processing strategy

Long flag	Short flag	Type	Default	Description
--strategy <strategy>	-s <strategy>	Enum (stats, interpolate)	stats	Processing strategy: compute statistics or interpolate signal
--alignment-type <alignment-type>	-	Enum (reference, query)	-	Only required if the alignment file contains both query- and reference-to-signal alignments. Set to determine which type will be processed
--skip-signal-norm	-	Flag	-	Skip z-standardization of signal intensity
--skip-dwell-norm	-	Flag	-	Skip z-standardization of dwell times

Strategy 1: stats

The following flag is only regarded if --strategy stats is set.

Long flag	Short flag	Type	Default	Description
--stats <stats>...	-	Enum(s) (mean, median, std, dwell, signal-to-noise)	mean std dwell	Statistics to compute per base when using --strategy stats. Multiple can be provided space-separated

Strategy 2: interpolate

The following flag is only regarded if --strategy interpolate is set. | Long flag | Short flag | Type | Default | Description |-|-|-|-|-| | --target-size <n> | - | Integer | 30 | Target size for interpolated signal chunks per base

Threading settings

Long flag	Short flag	Type	Default	Description
--threads <n>	-t <n>	Integer	8	Number of parallel threads
--queue-size <queue-size>	-	Integer	8000	Queue size for worker communication. Increase for higher memory-usage and possibly faster processing

Input/Output settings

Long flag	Short flag	Type	Default	Description
--input-chunk-size <n>	-	Integer	4000	Number of alignments read per iteration. Larger = faster, more memory
--force-overwrite	-f	Flag	-	Overwrite existing output file if it exists
--output-shape <shape>	-	Enum (melted, exploded, nested)	nested	Determines output structure (nested only for Parquet)
--output-batch-size <n>	-	Integer	4000	Number of processed alignments to buffer before writing to output file

Logging settings

Long flag	Short flag	Type	Default	Description
--log-level <log-level>	-	Enum (off, error, warn, info, debug, trace)	off	Controls verbosity of logging
--log-path <log-path>	Path (file)	log.txt	Log file path (used if --log-level != off)