debian man page for last-pair-probs

LAST-PAIR-PROBS.PY(1)						   User Commands					     LAST-PAIR-PROBS.PY(1)

NAME
       last-pair-probs.py - Read alignments of paired DNA reads to a genome

DESCRIPTION
   Usage:
	      last-pair-probs.py --help last-pair-probs.py [options] alignments1 alignments2

       Read  alignments  of  paired  DNA  reads to a genome, and estimate the probability that each alignment represents the genomic source of the
       read.

OPTIONS
       -h, --help
	      show this help message and exit

       -r, --rna
	      specifies that the reads are from potentially-spliced RNA

       -m M, --mismap=M
	      don't write alignment pairs with mismap probability > M (default: 0.01)

       -f BP, --fraglen=BP
	      mean fragment length in bp

       -s BP, --sdev=BP
	      standard deviation of fragment length

       -g BP, --genome=BP
	      haploid genome size in bp

       -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)

last-pair-probs.py 199						     May 2012						     LAST-PAIR-PROBS.PY(1)