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<HTML>
<HEAD>
<TITLE>bundlelinks - bundle neighbouring links together in an effort to reduce complexity of link structure</TITLE>
<LINK REV="made" HREF="mailto:root@gene0.cigenomics.bc.ca">
</HEAD>
<BODY>
<!-- INDEX BEGIN -->
<UL>
<LI><A HREF="#NAME">NAME</A>
<LI><A HREF="#SYNOPSIS">SYNOPSIS</A>
<LI><A HREF="#DESCRIPTION">DESCRIPTION</A>
<LI><A HREF="#OUTPUT">OUTPUT</A>
<LI><A HREF="#OPTIONS">OPTIONS</A>
<UL>
<LI><A HREF="#_max_gap">-max_gap</A>
<LI><A HREF="#_min_bundle_membership_strict">-min_bundle_membership, -strict</A>
<LI><A HREF="#_min_bundle_size">-min_bundle_size</A>
<LI><A HREF="#_min_bundle_identity">-min_bundle_identity</A>
</UL>
<LI><A HREF="#HISTORY">HISTORY</A>
<LI><A HREF="#BUGS">BUGS</A>
<LI><A HREF="#AUTHOR">AUTHOR</A>
<LI><A HREF="#CONTACT">CONTACT</A>
</UL>
<!-- INDEX END -->
<HR>
<P>
<HR>
<H1><A NAME="NAME">NAME</A></H1>
<P>
bundlelinks - bundle neighbouring links together in an effort to reduce
complexity of link structure
<P>
<HR>
<H1><A NAME="SYNOPSIS">SYNOPSIS</A></H1>
<P>
<PRE> bundlelinks -links linkfile.txt -max_gap NUM
{-min_bundle_membership NUM | -strict }
{-min_bundle_size NUM}
{-min_bundle_identity FRACTION}
</PRE>
<P>
<PRE> bundlelinks -links data/dog.vs.human.all.txt > data/dog.vs.human.bundles.txt
</PRE>
<P>
<HR>
<H1><A NAME="DESCRIPTION">DESCRIPTION</A></H1>
<P>
The purpose of this script is to turn a large set of links into a smaller
one by merging neighbouring links.
<P>
<HR>
<H1><A NAME="OUTPUT">OUTPUT</A></H1>
<P>
The script produces a new link file to STDOUT.
<P>
A tally is sent to STDERR that lists the following
<P>
<PRE> # 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%)
</PRE>
<P>
<HR>
<H1><A NAME="OPTIONS">OPTIONS</A></H1>
<P>
<HR>
<H2><A NAME="_max_gap">-max_gap</A></H2>
<P>
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
<P>
<PRE> chr( start(L1) ) == chr( start(L2) )
chr( end(L1) ) == chr( end(L2) )
</PRE>
<P>
<PRE> distance( start(L1), start(L2) ) <= MAX_GAP
distance( end(L1), end(L2) ) <= MAX_GAP
</PRE>
<P>
If a link does not have any acceptable adjacent neighbouring links, it
forms a single-link bundle.
<P>
<HR>
<H2><A NAME="_min_bundle_membership_strict">-min_bundle_membership, -strict</A></H2>
<P>
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).
<P>
The -strict option is equivalent to -min_bundle_membership 2.
<P>
<HR>
<H2><A NAME="_min_bundle_size">-min_bundle_size</A></H2>
<P>
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.
<P>
The minimum size parameter is applied independently to both ends of all
links in a bundle.
<P>
<HR>
<H2><A NAME="_min_bundle_identity">-min_bundle_identity</A></H2>
<P>
This parameter filters bundles based on the bundle identity, which is
defined as
<P>
<PRE> identity = size(merged links) / extent(merged links)
</PRE>
<P>
Both ends of the bundle are evaluated independently.
<P>
<HR>
<H1><A NAME="HISTORY">HISTORY</A></H1>
<UL>
<LI><STRONG><A NAME="item_16">16 July 2008</A></STRONG>
<P>
Started and versioned.
</UL>
<P>
<HR>
<H1><A NAME="BUGS">BUGS</A></H1>
<P>
<HR>
<H1><A NAME="AUTHOR">AUTHOR</A></H1>
<P>
Martin Krzywinski
<P>
<HR>
<H1><A NAME="CONTACT">CONTACT</A></H1>
<P>
<PRE> Martin Krzywinski
Genome Sciences Centre
Vancouver BC Canada
www.bcgsc.ca
martink@bcgsc.ca
</PRE>
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