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PROGRAM:

NAME


last-pair-probs - Read alignments of paired DNA reads to a genome, and do estimations

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

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