bundlelinks - bundle neighbouring links together in an effort to reduce complexity of link structure

- NAME
- SYNOPSIS
- DESCRIPTION
- OUTPUT
- OPTIONS
  - -max_gap
  - -min_bundle_membership, -strict
  - -min_bundle_size
  - -min_bundle_identity
- HISTORY
- BUGS
- AUTHOR
- CONTACT

# NAME

bundlelinks - bundle neighbouring links together in an effort to reduce complexity of link structure

# SYNOPSIS

      bundlelinks -links linkfile.txt -max_gap NUM
                  {-min_bundle_membership NUM | -strict }
                  {-min_bundle_size NUM}
                  {-min_bundle_identity FRACTION}

      bundlelinks -links data/dog.vs.human.all.txt > data/dog.vs.human.bundles.txt

# DESCRIPTION

The purpose of this script is to turn a large set of links into a smaller one by merging neighbouring links.

# OUTPUT

The script produces a new link file to STDOUT.

A tally is sent to STDERR that lists the following

      # total number of links read in
      num_links 39978
      # number of links in initial bundles (filtered for membership)
      num_links_in_init_bundles 39839
      # total number of initial bundles
      num_init_bundles 524
      # number of accepted bundles (filtered for both size and membership)
      num_passed_bundles 277 (52.86%)
      # number of links in accepted bundles
      num_links_in_passed_bundles 36732 (92.20%)

# OPTIONS

## -max_gap

Adjacent links are merged into bundles if their start/end coordinates are sufficiently close. Given two links L1 and L2, they are merged into a bundle if

      chr( start(L1) ) == chr( start(L2) )
      chr( end(L1) ) == chr( end(L2) )

      distance( start(L1), start(L2) ) <= MAX_GAP
      distance( end(L1), end(L2) ) <= MAX_GAP

If a link does not have any acceptable adjacent neighbouring links, it forms a single-link bundle.

## -min_bundle_membership, -strict

These parameters filter bundles with few links. You can set the minimum number of links required in a bundle for the bundle to be accepted (-min_bundle_membership).

The -strict option is equivalent to -min_bundle_membership 2.

## -min_bundle_size

In addition to, or in place of, filtering bundles based on the number of links they comprise, you can accept bundles based on the size of the links in the bundle.

The minimum size parameter is applied independently to both ends of all links in a bundle.

## -min_bundle_identity

This parameter filters bundles based on the bundle identity, which is defined as

     identity = size(merged links) / extent(merged links)

Both ends of the bundle are evaluated independently.

# HISTORY

- 16 July 2008

  Started and versioned.

# BUGS

# AUTHOR

Martin Krzywinski

# CONTACT

      Martin Krzywinski
      Genome Sciences Centre
      Vancouver BC Canada
      www.bcgsc.ca
      martink@bcgsc.ca