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