SYNOPSIS

last-pair-probs/ [options] interleaved-alignments

last-pair-probs/ [options] alignments1 alignments2

DESCRIPTION

Read alignments of paired DNA reads to a genome, and: (1) estimate the distribution of distances between paired reads, (2) estimate the probability that each alignment represents the genomic source of the read.

OPTIONS

-h, --help

show this help message and exit

-r, --rna

assume the reads are from potentially-spliced RNA

-e, --estdist

just estimate the distribution of distances

-m M, --mismap=,M/

don't write alignments with mismap probability > M (default: 0.01)

-f BP, --fraglen=,BP/

mean distance in bp

-s BP, --sdev=,BP/

standard deviation of distance

-d PROB, --disjoint=,PROB/

prior probability of disjoint mapping (default: 0.02 if -r, else 0.01)

-c CHROM, --circular=,CHROM/

specifies that chromosome CHROM is circular (default: chrM)

-V, --version

show program's version number and exit