help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

Estimation method

set

Estimates error statistics within annotation sets.

barcode

Calculates pairwise distance metrics of barcode sequences.

output files:

error-position

estimated error by read position.

error-quality

estimated error by the quality score assigned within the input file.

error-nucleotide

estimated error by nucleotide.

error-set

estimated error by annotation set size.

distance-set

pairwise hamming distances by annotation set.

threshold-set

thresholds from pairwise hamming distances for annotation sets.

distance-barcode

estimated error by pairwise hamming distances

threshold-barcode

thresholds from pairwise hamming distances for clustering barcodes

output fields:

POSITION

read position with base zero indexing.

Q

Phred quality score.

OBSERVED

observed nucleotide value.

REFERENCE

consensus nucleotide for the barcode read group.

SET_COUNT

barcode read group size.

REPORTED_Q

mean Phred quality score reported within the input file for the given position, quality score, nucleotide or read group.

MISMATCHES

count of observed mismatches from consensus for the given position, quality score, nucleotide or read group.

OBSERVATIONS

total count of observed values for each position, quality score, nucleotide or read group size.

ERROR

estimated error rate.

EMPIRICAL_Q

estimated error rate converted to a Phred quality score.

ALL

histogram (count) of all pairwise distance distribution.

DTN

histogram (count) of distance to nearest distribution.

DISTANCE

length normalized hamming distance.