[med-svn] r1437 - in trunk/packages: . fastlink fastlink/trunk fastlink/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Mon Feb 18 16:21:27 UTC 2008
Author: tille
Date: 2008-02-18 16:21:26 +0000 (Mon, 18 Feb 2008)
New Revision: 1437
Added:
trunk/packages/fastlink/
trunk/packages/fastlink/trunk/
trunk/packages/fastlink/trunk/debian/
trunk/packages/fastlink/trunk/debian/README.Debian
trunk/packages/fastlink/trunk/debian/changelog
trunk/packages/fastlink/trunk/debian/compat
trunk/packages/fastlink/trunk/debian/control
trunk/packages/fastlink/trunk/debian/control.in
trunk/packages/fastlink/trunk/debian/copyright
trunk/packages/fastlink/trunk/debian/datafile.5
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.alleles
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.autoselect
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.avoid-recomp
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.fastlink
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.loops
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization2
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.random
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.traverse
trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.unknown
trunk/packages/fastlink/trunk/debian/fastlink-doc.docs
trunk/packages/fastlink/trunk/debian/fastlink.docs
trunk/packages/fastlink/trunk/debian/fastlink.html
trunk/packages/fastlink/trunk/debian/fastlink.install
trunk/packages/fastlink/trunk/debian/fastlink.manpages
trunk/packages/fastlink/trunk/debian/get-orig-source
trunk/packages/fastlink/trunk/debian/ilink.1
trunk/packages/fastlink/trunk/debian/ilink.desktop
trunk/packages/fastlink/trunk/debian/linkage.5
trunk/packages/fastlink/trunk/debian/linkmap.1
trunk/packages/fastlink/trunk/debian/linkmap.desktop
trunk/packages/fastlink/trunk/debian/lodscore.1
trunk/packages/fastlink/trunk/debian/lodscore.desktop
trunk/packages/fastlink/trunk/debian/mlink.1
trunk/packages/fastlink/trunk/debian/mlink.desktop
trunk/packages/fastlink/trunk/debian/pedfile.5
trunk/packages/fastlink/trunk/debian/rules
trunk/packages/fastlink/trunk/debian/unknown.1
trunk/packages/fastlink/trunk/debian/unknown.desktop
Log:
Check in old packaging + get-orig-source script. Update for group maintenance will follow
Added: trunk/packages/fastlink/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fastlink/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/fastlink/trunk/debian/README.Debian 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,15 @@
+fastlink for Debian
+----------------------
+
+I uncompressed and untared the downloaded latest archive fastlink.tar.Z,
+renamed the resulting directory to fastlink-4.1P-fix81 (because of the last
+bugfix with no. 81), and made a new tarball fastlink-4.1P-fix81.tar.gz which
+was then used for upgrading the previous Debian package version with uupdate.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org>, Sat, 12 May 2001 18:43:26 +0200
+
+I just adopted this procedure in naming the orig.tar.gz file.
+Moreover I removed some files which are very specific for running
+fastlink on AIX, VMS and IRIX just to save some disk space.
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 Apr 2003 09:51:31 +0200
Added: trunk/packages/fastlink/trunk/debian/changelog
===================================================================
--- trunk/packages/fastlink/trunk/debian/changelog (rev 0)
+++ trunk/packages/fastlink/trunk/debian/changelog 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,115 @@
+fastlink (4.1P-fix92-1) unstable; urgency=low
+
+ * New upstream fix package
+ * Standards-Version: 3.7.2 (no changes necessary)
+ * Switched to cdbs
+ * Setting DebTags
+ * Added desktop files
+
+ -- Andreas Tille <tille at debian.org> Sat, 9 Sep 2006 12:52:33 +0200
+
+fastlink (4.1P-fix91-1) unstable; urgency=low
+
+ * New bugfix release
+ * removed some files which are very specific for running fastlink on
+ AIX, VMS and IRIX from source package which had to be repackaged anyway.
+ * Standards-Version: 3.6.1.1
+
+ -- Andreas Tille <tille at debian.org> Wed, 1 Dec 2004 14:19:29 +0100
+
+fastlink (4.1P-fix88-3) unstable; urgency=low
+
+ * Fixed maintainer address in debian/control
+ closes: #195322
+ * Patched 4.1P/src/{commondefs,unknown}.h to replace varargs.h by stdarg.h
+ Ported functions in iostuff.c to get rid of va_* stuff. Many thanks to
+ Colin Watson <cjwatson at debian.org> for his patches.
+ Replaced <sys/time.h> by <time.h>
+ These points fix FTBFS with gcc-3.3.
+ closes: #194913
+
+ -- Andreas Tille <tille at debian.org> Mon, 2 Jun 2003 09:27:22 +0200
+
+fastlink (4.1P-fix88-2) unstable; urgency=low
+
+ * What difference does it make to the dead, the orphans and the homeless,
+ whether the mad destruction is wrought under the name of totalitarianism
+ or the holy name of liberty or democracy?
+ -- Mahatma Gandhi (1869 - 1948), "Non-Violence in Peace and War"
+ * Added manpages for data formats and replaced unknown.1. These
+ pages were kindly provided by Elizabeth Barham
+ <lizzy at soggytrousers.net>
+ * fastlink-doc now only suggests fastlink
+ * Added doc-base entries.
+ * CHanged compile time option from -g to -Wall
+
+ -- Andreas Tille <tille at debian.org> Sat, 26 Apr 2003 13:50:38 +0200
+
+fastlink (4.1P-fix88-1) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * New upstream release (bugfixes)
+ * New maintainer
+ closes: #100221
+ * Build-Depends: debhelper (>= 4.0)
+ * Standards-Version: 3.5.9
+ * debian/compat now stores debhelper compatibility version
+ * Compliant to developers reference "6.3.2. Upstream home page" and
+ XBCS-URL: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+ * Updated fastlink.html from web page
+ * Wrote manpages.
+ * Removed the following files from binary package because they just describe
+ Infromation for compilation and installation:
+ README.AIX README.ALPHAVMS README.DOS README.Digital README.IRIX README.VAX
+ README.VMS README.djgpp README.install README.makefile README.portability
+ * Split up into two packages to remove papers from the binary package.
+ This reduces space on Debian mirrors because the main part of the
+ binary package was architecture "all" and probably saves disk space for
+ local installs were these docs are not needed.
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 Apr 2003 09:51:31 +0200
+
+fastlink (4.1P-fix81-2) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Fri, 24 Aug 2001 23:06:48 +0200
+
+fastlink (4.1P-fix81-1) unstable; urgency=low
+
+ * New upstream release (upstream used the same version number 4.1P, but
+ introduced some new bugfixes incl. 78-81); closes: #43471
+ * Enclosed the fastlink homepage to docs, and a README.Debian.
+ * Updated Debian package internals.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Sat, 12 May 2001 18:43:26 +0200
+
+fastlink (4.1P-2) unstable; urgency=low
+
+ * Adopted by new maintainer; closes: #92804
+ * Removed several unnecessary files in debian subdirectory.
+ * Updated to latest standards version and added Build-Depends (changed
+ control, copyright, dirs, docs, and rules);
+ closes: #91154, #91441, #42712
+ * Moved package from misc to section science, because it is a tool that
+ is exclusively useful for biologists.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Sat, 21 Apr 2001 09:17:46 +0200
+
+fastlink (4.1P-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Mon, 19 Jul 1999 17:39:24 +0200
+
+fastlink (4.0P-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Fri, 5 Feb 1999 15:36:21 +0100
+
+Local variables:
+mode: debian-changelog
+End:
Added: trunk/packages/fastlink/trunk/debian/compat
===================================================================
--- trunk/packages/fastlink/trunk/debian/compat (rev 0)
+++ trunk/packages/fastlink/trunk/debian/compat 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1 @@
+5
Added: trunk/packages/fastlink/trunk/debian/control
===================================================================
--- trunk/packages/fastlink/trunk/debian/control (rev 0)
+++ trunk/packages/fastlink/trunk/debian/control 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,28 @@
+Source: fastlink
+Section: science
+Priority: optional
+Maintainer: Andreas Tille <tille at debian.org>
+Build-Depends: cdbs (>= 0.4.23-1.1), debhelper (>= 5)
+Standards-Version: 3.7.2
+XBCS-URL: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+
+Package: fastlink
+Architecture: any
+Depends: ${shlibs:Depends}
+Suggests: fastlink-doc
+Description: [Biology] A faster version of pedigree programs of Linkage
+ Fastlink is much faster than the original Linkage but does not
+ implement all the programs.
+ .
+ Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+XB-Tag: suite::debian-med:bio, legacy::science, made-of::lang:c
+
+Package: fastlink-doc
+Architecture: all
+Suggests: fastlink
+Description: [Biology] Some papers about fastlink
+ You do not really need these papers about fastlink but it is highly
+ recommended to study this documentation before starting with the
+ tools of the fastlink package.
+ .
+ Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
Added: trunk/packages/fastlink/trunk/debian/control.in
===================================================================
--- trunk/packages/fastlink/trunk/debian/control.in (rev 0)
+++ trunk/packages/fastlink/trunk/debian/control.in 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,28 @@
+Source: fastlink
+Section: science
+Priority: optional
+Maintainer: Andreas Tille <tille at debian.org>
+Build-Depends: @cdbs@
+Standards-Version: 3.7.2
+XBCS-URL: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+
+Package: fastlink
+Architecture: any
+Depends: ${shlibs:Depends}
+Suggests: fastlink-doc
+Description: [Biology] A faster version of pedigree programs of Linkage
+ Fastlink is much faster than the original Linkage but does not
+ implement all the programs.
+ .
+ Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+XB-Tag: suite::debian-med:bio, legacy::science, made-of::lang:c
+
+Package: fastlink-doc
+Architecture: all
+Suggests: fastlink
+Description: [Biology] Some papers about fastlink
+ You do not really need these papers about fastlink but it is highly
+ recommended to study this documentation before starting with the
+ tools of the fastlink package.
+ .
+ Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
Added: trunk/packages/fastlink/trunk/debian/copyright
===================================================================
--- trunk/packages/fastlink/trunk/debian/copyright (rev 0)
+++ trunk/packages/fastlink/trunk/debian/copyright 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,14 @@
+This package was debianized by Andreas Tille <tille at debian.org> on
+Wed, 1 Dec 2004 14:19:29 +0100.
+
+It was downloaded from ftp://fastlink.nih.gov/pub/fastlink/fastlink.tar.Z
+Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+
+Upstream Author: Alejandro Schaffer <schaffer at nchgr.nih.gov>
+
+Copyright: GPL
+
+You are free to distribute this software under the terms of
+the GNU General Public Licence.
+On Debian systems, the complete text of the GNU General Public
+Licence can be found in /usr/share/common-licenses/GPL file.
Added: trunk/packages/fastlink/trunk/debian/datafile.5
===================================================================
--- trunk/packages/fastlink/trunk/debian/datafile.5 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/datafile.5 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,404 @@
+.TH DATAFILE 5 "April 22, 2003"
+.SH NAME
+DATAFILE \- LINKAGE's DATAFILE
+.SH DESCRIPTION
+Descriptions of loci and other information are contained in
+.BR DATAFILE (5).
+The information in this file is divided into four parts
+.IP 1. 5
+general information on loci and locus order;
+.IP 2. 5
+description of loci;
+.IP 3. 5
+information on recombination;
+.IP 4. 5
+program-specific information.
+.PP
+In explaining the structure of
+.BR DATAFILE (5)
+we will use two concepts of
+locus order. The first is the input order, or the order in which the
+phenotypes corresponding to the loci appear in
+.BR PEDFILE (5).
+The second is chromosome order, or the physical order assumed
+for the loci. The input order is fixed once
+.BR PEDFILE (5)
+is created, but the chromosome order can be changed to test various
+hypotheses.
+
+Various parameters such as recombination rates, gene frequencies,
+penetrances, etc., are specified in the
+.BR DATAFILE (5).
+These refer to the initial values of these parameters. The analysis
+programs can modify some of these values for specific purposes,
+e.g. maximum likelihood estimation.
+
+.SH EXAMPLE
+
+Before we attempt to explain the format of various parts of the
+DATAFILE, it is useful to consider a complete file as an example. The
+following is the DATAFILE for three sex-linked loci, one of which is
+Duchenne muscular dystrophy; creatine kinase measurements are
+available for heterozygote testing in women:
+
+ 3 0 1 5 << no loci, risk locus, sexlinked (if 1), program code
+ 3 0.001 0.001 0 << mut locus, mut mal, mut fem, hap freq (if 1)
+
+ 1 3 2 << order of loci
+
+ 2 2 <<< binary factors, # alleles
+ 5.00000E-01 5.00000E-01 << gene freqs
+ 2 << number of binary factors
+ 1 0
+ 0 1 << allelic codes
+
+ 2 2 <<< binary factors, # alleles
+ 5.00000E-01 5.00000E-01 << gene freqs
+ 2 << number of binary factors
+ 1 0
+ 0 1 << allelic codes
+
+ 0 2 <<< quan, # alleles
+ 9.99800E-01 2.00000E-04 << gene freqs
+ 1 << number of traits
+ 1.57000E+00 2.10000E+00 2.10000E+00 << genotype means
+ 5.90000E-02 << variance
+ 2.90000E+00 << multiplier for variance in heterozygotes
+ 0 0 << sex difference (if 1) and interference (if 1)
+ 0.1 0.1 << recombination values
+ 1 0.5 0.5
+
+The last line contains information for the
+.BR mlink (1)
+program; this is indicated by the program code 5 on the first
+line. Other parameters are specified as indicated in the comments
+following certain lines (indicated by << ). Comments are allowed on
+some lines for easy interpretation of the file.
+
+.SS "Loci and Locus Order"
+The first two lines of DATAFILE contain information on a variety of
+parameters, including the number of loci (nlocus), a risk locus
+(risklocus), sex-linked or autosomal data (sexlink), a mutation locus
+(mutsys) and mutation rates (mutmale and mutfem ), linkage
+disequilibrium (disequil ), and a program code (nprogram). The first
+two lines are followed by a third line giving the chromosome order for
+the loci. The format is:
+
+ nlocus risklocus sexlink nprogram
+ mutsys mutmale mutfem disequil
+ (chromosome order)
+
+Mutsys and the chromosome order of the loci must begin on new lines;
+comments can follow at the end of each line. Nprogram is not used by
+the LINKAGE programs, but is required for interfacing with the shell
+program LCP. It is used to describe the program for which the file is
+constructed. LCP can use files constructed for one program as input
+for a different program. Therefore the datafile is not changed for
+different programs when using LCP.
+
+.TS
+box center ;
+c|l.
+Variable Name Valid Values
+_
+nlocus T{
+1 to maxlocus (as specified by a constant in the programs)
+T}
+_
+risklocus T{
+0 if risk is not to be calculated
+T}
+ _
+ T{
+disease locus number (input order) if risk is to be calculated
+T}
+_
+sexlink T{
+0 for autosomal data
+T}
+ _
+ T{
+1 for sex-linked data
+T}
+_
+nprogram 1 CILINK
+ _
+ 2 CMAP
+ _
+ 3 ILINK
+ _
+ 4 LINKMAP
+ _
+ 5 MLINK
+ _
+ 6 LODSCORE
+ _
+ 7 CLODSCORE
+_
+mutsys T{
+0 if mutation rates are zero
+T}
+ _
+ T{
+mutation locus number (input order) for non-zero mutation rates
+T}
+_
+mutmale male mutation rate
+_
+mutfem female mutation rate
+_
+disequil T{
+0 if loci are assumed to be in linkage equilibrium
+T}
+ _
+ T{
+1 if loci are in linkage disequilibrium
+T}
+.TE
+
+When loci are in linkage equilibrium, allele frequencies must be given
+under each locus description; otherwise, haplotype frequencies are
+provided. When risk is calculated, a disease allele is provided in the
+locus description for the "risklocus." As an example, consider the
+analysis of 3 autosomal loci in the chromosome order 1 3 2. The first
+three lines of the DATAFILE could be:
+
+ 3 0 0 3 << no loci, risk locus, sexlinked (if 1), program code
+ 3 0.1 0.1 0 << mut locus, mut mal, mut fem, haplotype freq (if 1)
+ 1 3 2 << order of loci
+
+The data are autosomal with mutation at the third locus.
+.SS "Description of Loci"
+The loci are described in the order in which they appear in the
+.BR PEDFILE (5).
+Assuming linkage equilibrium, the gene frequencies are specified as
+part of the locus description (linkage disequilibrium will be
+documented in a later version). The descriptions differ according to
+the type of locus. A numeric code distinguishes each of the types:
+
+.TS
+box center;
+n|l.
+0 Quantitative variable
+_
+1 Affection status
+_
+2 Binary factors
+_
+3 Numbered alleles
+.TE
+
+The format for each locus type, assuming linkage equilibrium, is as follows:
+.SS "Numbered alleles"
+The locus description consists of two lines. The first gives the code
+for numbered alleles and the total number of alleles. The second gives
+the gene frequencies. For example:
+
+ 3 2 << numbered alleles code, total number of alleles
+ 0.5 0.5 << gene frequencies
+
+specifies two alleles with equal gene frequencies.
+
+.SS "Binary factors"
+The first two lines are similar to those in the previous
+example. After this the number of factors is specified on a separate
+line, followed by one line for each allele specification. As an
+example, consider the case of a recessive trait:
+
+ 2 2 << binary factor code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 2 << number of factors
+ 1 1
+ 0 1 << alleles
+
+.SS "Affection status"
+
+The number of liability classes replaces the number of factors, and
+penetrances are given for each genotype in each class:
+
+ 1 2 << affection status code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 1 << number of liability classes
+ 0.0 1.0 1.0 << penetrances
+
+describes a fully penetrant, dominant disease locus. The genotypes are
+in the order 11, 12, 22 where 1 is the first allele and 2 is the
+second allele specified in the gene frequency list. For three alleles,
+the genotype order is 11, 12, 13, 22, 23, 33. The same pattern is
+followed for more alleles. To describe a similar locus, but with
+reduced penetrance and two liability classes, use the following:
+
+ 1 2 << affection status code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 2 << number of liability classes
+ 0.0 0.5 0.5
+ 0.0 0.9 0.9 << penetrances
+
+With sex-linked data, male penetrances must also be defined for each
+allele. The following describes a sex-linked disease with 50%
+penetrance in males:
+
+ 1 2 << affection status code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 1 << number of liability classes
+ 0.0 0.0 1.0
+ 0.0 0.5 << female followed by male penetrances
+
+.SS "Quantitative trait"
+
+Quantitative traits are described by a first line containing the
+quantitative code (0) and the number of alleles, and a second line
+with gene frequencies, as in the previous examples. These are followed
+by lines indicating the number of quantitative variables, genotypic
+means for each variable, a variance-covariance matrix, and a constant
+that gives the ratio of variance-covariance in heterozygotes to
+homozygotes.
+
+For a single quantitative variable, the format is:
+
+ 0 2 << quantitative variable code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 1 << number of quantitative variables
+ 10.0 12.0 14.0 << genotypic means
+ 1.5 << variance
+ 1.0 << multiplier for heterozygote variance
+
+The genotypes are 1/1, 1/2 and 2/2, respectively, where allele 1 has
+the frequency 0.999. For two quantitative variables, the description
+is:
+
+ 0 2 << quantitative variable code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 2 << number of liability classes
+ 10.0 12.0 14.0
+ -10.0 0.0 10.0 << genotypic means
+ 1.5 10.0 100.0 << variance-covariance
+ 1.0 << multiplier for heterozyg. variance-covariance
+
+Only the upper triangle of the variance-covariance matrix is given;
+the order is V11, V12, V13 ... V22, V23 ... etc. Here, the variance of
+the first variable is 1.5, the covariance is 10.0, and the variance of
+the second variable is 100.0. When describing the "risk locus," the
+disease allele (risk allele) must be designated at the end of the
+locus description. For example:
+
+ 1 2 << affection status code, number of alleles
+ 0.999 0.001 << gene frequencies
+ 1 << number of liability classes
+ 0.0 1.0 1.0 << penetrances
+ 2 << risk allele
+
+.SS "Recombination Information"
+
+In addition to recombination rates, sex-differences and interference
+must be specified in this section. Sex-difference options are
+indicated by an integer variable that takes the following values:
+
+.TS
+box center;
+n|l.
+0 T{
+no sex-difference
+T}
+_
+1 T{
+constant sex-difference (the ratio of female/male genetic distance is
+the same in all intervals)
+T}
+_
+2 T{
+variable sex-difference (the female/male distance ratio can be
+different in each interval)
+T}
+.TE
+
+The interference option can take the following values:
+
+.TS
+box center;
+n|l.
+0 T{
+no interference
+T}
+_
+1 T{
+interference without a mapping function
+T}
+_
+2 T{
+user-specified mapping function
+T}
+.TE
+
+Interference (i.e. options 1 or 2) is allowed only in some analysis
+programs with three loci. The programs, as distributed, contain
+Kosambi interference as the user-specified mapping function.
+
+First, consider a case without interference. When the sex-difference
+is "0," one recombination rate is given for each of the nlocus-1
+segments (see the complete example above). If the sex-difference
+option is "1," the male recombination rates are given on one line, and
+the female/male genetic distance is specified on the next line, e.g.:
+
+ 1 0 << sex difference, interference
+ 0.1 0.2 0.1 << male recombination
+ 2.0 << female/male ratio of genetic distance
+
+When the sex-difference option is "2", the male recombination rates
+are followed on the next line by female recombination rates:
+
+ 2 0 << sex difference, interference
+ 0.1 0.2 0.1 << male recombination
+ 0.2 0.1 0.2 << female recombination
+
+Interference can be specified for three loci. With the interference
+option 1, three recombination rates are given. These are the
+recombination rates between adjacent loci in the two segments and the
+recombination rate between the flanking loci. An example is:
+
+ 1 1 << sex difference, interference
+ 0.1 0.1 0.18 << male recombination
+ 2.0 << female/male ratio of genetic distance
+
+With the interference option 2, only the rates between the adjacent
+loci are provided:
+
+ 1 2 << sex difference, interference
+ 0.1 0.1 << male recombination
+ 2.0 << female/male ratio of genetic distance
+
+.SS "Program-specific information"
+The program-specific information consists of a series of lines at the
+end of the
+.BR DATAFILE (1)
+describing which parameters should be varied iteratively by the
+analysis programs.
+.SH NOTES
+The information contained herein was gleaned, often-times verbatim,
+from
+.UR http://linkage.rockefeller.edu/soft/linkage/
+the LINKAGE User's Guide
+.UE
+on the web by kind permission of Jurg Ott, Ph.D.
+
+.SH AUTHORS
+Mark Lathrop and Jurg Ott.
+.PP
+This manual page was written by Elizabeth Barham
+<lizzy at soggytrousers.net> for the Debian GNU/Linux distribution.
+
+.SH WORLD-WIDE-WEB
+.UR http://linkage.rockefeller.edu/soft/linkage/
+http://linkage.rockefeller.edu/soft/linkage/
+.UE
+
+.SH SEE ALSO
+.BR LINKAGE (5),
+.BR PEDFILE (5),
+.BR ilink (1),
+.BR linkmap (1),
+.BR lodscore (1),
+.BR mlink (1),
+and
+.BR unknown (1).
+
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.alleles
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.alleles (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.alleles 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,10 @@
+Document: fastlink-alleles
+Title: Faster Linkage Analysis Computations for Pedigrees with Loops or Unused Alleles
+Author: Alejandro A. Schäffer
+Abstract: This document describes the implementation in FASTLINK of some
+ algorithmic improvements to partly address the problems of pedigree loops
+ and unknown genotypes.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper5.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.autoselect
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.autoselect (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.autoselect 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,10 @@
+Document: fastlink-autoselect
+Title: Automatic Selection of Loop Breakers for Genetic Linkage Analysis
+Author: Ann Becker, Dan Geiger, Alejandro A. Schäffer
+Abstract: This document describes how the LINKAGE program was enhanced
+ by an automated process of selecting loop breakers by an hybrid algorithm
+ in the FASTLINK program.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper6.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.avoid-recomp
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.avoid-recomp (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.avoid-recomp 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,9 @@
+Document: fastlink-avoid-recomp
+Title: Avoiding Recomputation in Linkage Analysis
+Author: Alejandro A. Schäffer, Sandeep K. Gupta, K. Shriram, Robert W. Cottingham Jr.
+Abstract: This document describes improvements over the original LINKAGE
+ program which were applied in fastlink.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper2.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.fastlink
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.fastlink (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.fastlink 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,10 @@
+Document: fastlink
+Title: Faster Sequential Genetic Linkage Computations
+Author: Robert W. Cottingham Jr., Ramana M. Idury, Alejandro A. Schäffer
+Abstract: This document describes the basics of the fastlink allgorithm
+ which is based on linkage analysis using maximum likelihood estimation
+ which is a powerful tool for locating genes.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper1.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.loops
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.loops (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.loops 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,8 @@
+Document: fastlink-loops
+Title: Loops in Fastlink
+Author: Alejandro A. Schäffer
+Abstract: This document describes some aspects of pedigree loops in fastlink.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/loops.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,9 @@
+Document: fastlink-parallelization
+Title: Parallelization of General Linkage Analysis Problems
+Author: Sandhya Dwarkadas, Alejandro A. Schäffer, et. all.
+Abstract: This document describes a parallel implementation of a
+ linkage analysis program.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper3.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization2
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization2 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.parallelization2 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,10 @@
+Document: fastlink-parallelization2
+Title: Integrating Parallelization Strategies for Linkage Analysis
+Author: Sandeep K. Gupta, Alejandro A. Schäffer, Alan L. Cox, Sandhya Dwarkadas
+Abstract: This document describes a second parallel implementation of the
+ ILINK program from the LINKAGE package that improves the previous
+ implementation.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper4.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.random
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.random (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.random 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,9 @@
+Document: fastlink-random
+Title: Random Algorithms for the Loop Cutset Problem
+Author: Ann Becker, Dan Geiger, Alejandro A. Schäffer
+Abstract: This document describes how to find a minimum loop cutset in a
+ Bayesian network with high probability.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/paper7.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.traverse
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.traverse (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.traverse 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,9 @@
+Document: fastlink-traverse
+Title: Pedigree Traversal in Fastlink
+Author: Alejandro A. Schäffer
+Abstract: This document describes some aspects of pedigree traversal in
+ Fastlink.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/traverse.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.unknown
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.unknown (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.doc-base.unknown 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,9 @@
+Document: fastlink-unknown
+Title: The Mystery of Unknown
+Author: Alejandro A. Schäffer
+Abstract: This document describes some aspects of the UNKNOWN auxiliary
+ program that is distributed with the fastlink package.
+Section: Apps/Science
+
+Format: postscript
+Files: /usr/share/doc/fastlink-doc/unknown.ps.gz
Added: trunk/packages/fastlink/trunk/debian/fastlink-doc.docs
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink-doc.docs (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink-doc.docs 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1 @@
+*.ps
Added: trunk/packages/fastlink/trunk/debian/fastlink.docs
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink.docs (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink.docs 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,18 @@
+README
+README.ILINK
+README.Linux
+README.TreadMarks
+README.allele
+README.bugreport
+README.checkpoint
+README.constants
+README.mapfun
+README.memory
+README.p4
+README.parallel
+README.scaling
+README.time
+README.trouble
+README.unknown
+README.updates
+debian/fastlink.html
Added: trunk/packages/fastlink/trunk/debian/fastlink.html
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink.html (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink.html 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,360 @@
+<html>
+<head>
+ <title>FASTLINK Home Page</title>
+
+<script LANGUAGE="JavaScript">
+<!-- hide JavaScript from non-JavaScript browsers
+// Ultimate client-side JavaScript client sniff.
+// (C) Netscape Communications 1999. Permission granted to reuse and distribute.
+
+// Everything you always wanted to know about your JavaScript client
+// but were afraid to ask. Creates "is_" variables indicating:
+// (1) browser vendor:
+// is_nav, is_ie, is_opera
+// (2) browser version number:
+// is_major (integer indicating major version number: 2, 3, 4 ...)
+// is_minor (float indicating full version number: 2.02, 3.01, 4.04 ...)
+// (3) browser vendor AND major version number
+// is_nav2, is_nav3, is_nav4, is_nav4up, is_nav5, is_nav5up, is_ie3, is_ie4, is_ie4up
+// (4) JavaScript version number:
+// is_js (float indicating full JavaScript version number: 1, 1.1, 1.2 ...)
+// (5) OS platform and version:
+// is_win, is_win16, is_win32, is_win31, is_win95, is_winnt, is_win98
+// is_os2
+// is_mac, is_mac68k, is_macppc
+// is_unix
+// is_sun, is_sun4, is_sun5, is_suni86
+// is_irix, is_irix5, is_irix6
+// is_hpux, is_hpux9, is_hpux10
+// is_aix, is_aix1, is_aix2, is_aix3, is_aix4
+// is_linux, is_sco, is_unixware, is_mpras, is_reliant
+// is_dec, is_sinix, is_freebsd, is_bsd
+// is_vms
+//
+
+ var agt=navigator.userAgent.toLowerCase();
+
+ var is_major = parseInt(navigator.appVersion);
+ var is_minor = parseFloat(navigator.appVersion);
+
+ var is_nav = ((agt.indexOf('mozilla')!=-1) && (agt.indexOf('spoofer')==-1)
+ && (agt.indexOf('compatible') == -1) && (agt.indexOf('opera')==-1)
+ && (agt.indexOf('webtv')==-1));
+ var is_nav2 = (is_nav && (is_major == 2));
+ var is_nav3 = (is_nav && (is_major == 3));
+ var is_nav4 = (is_nav && (is_major == 4));
+ var is_nav4up = (is_nav && (is_major >= 4));
+ var is_navonly = (is_nav && ((agt.indexOf(";nav") != -1) ||
+ (agt.indexOf("; nav") != -1)) );
+ var is_nav5 = (is_nav && (is_major == 5));
+ var is_nav5up = (is_nav && (is_major >= 5));
+
+ var is_ie = (agt.indexOf("msie") != -1);
+ var is_ie3 = (is_ie && (is_major < 4));
+ var is_ie4 = (is_ie && (is_major == 4) && (agt.indexOf("msie 5.0")==-1) );
+ var is_ie4up = (is_ie && (is_major >= 4));
+ var is_ie5 = (is_ie && (is_major == 4) && (agt.indexOf("msie 5.0")!=-1) );
+ var is_ie5up = (is_ie && !is_ie3 && !is_ie4);
+
+ var is_aol = (agt.indexOf("aol") != -1);
+ var is_aol3 = (is_aol && is_ie3);
+ var is_aol4 = (is_aol && is_ie4);
+
+ var is_opera = (agt.indexOf("opera") != -1);
+ var is_webtv = (agt.indexOf("webtv") != -1);
+
+ var is_js;
+ if (is_nav2 || is_ie3) is_js = 1.0
+ else if (is_nav3 || is_opera) is_js = 1.1
+ else if ((is_nav4 && (is_minor <= 4.05)) || is_ie4) is_js = 1.2
+ else if ((is_nav4 && (is_minor > 4.05)) || is_ie5) is_js = 1.3
+ else if (is_nav5) is_js = 1.4
+ else if (is_nav && (is_major > 5)) is_js = 1.4
+ else if (is_ie && (is_major > 5)) is_js = 1.3
+ else is_js = 0.0;
+
+ var is_win = ( (agt.indexOf("win")!=-1) || (agt.indexOf("16bit")!=-1) );
+ var is_win95 = ((agt.indexOf("win95")!=-1) || (agt.indexOf("windows 95")!=-1));
+
+ var is_win16 = ((agt.indexOf("win16")!=-1) ||
+ (agt.indexOf("16bit")!=-1) || (agt.indexOf("windows 3.1")!=-1) ||
+ (agt.indexOf("windows 16-bit")!=-1) );
+
+ var is_win31 = ((agt.indexOf("windows 3.1")!=-1) || (agt.indexOf("win16")!=-1) ||
+ (agt.indexOf("windows 16-bit")!=-1));
+
+ var is_win98 = ((agt.indexOf("win98")!=-1) || (agt.indexOf("windows 98")!=-1));
+ var is_winnt = ((agt.indexOf("winnt")!=-1) || (agt.indexOf("windows nt")!=-1));
+ var is_win32 = (is_win95 || is_winnt || is_win98 ||
+ ((is_major >= 4) && (navigator.platform == "Win32")) ||
+ (agt.indexOf("win32")!=-1) || (agt.indexOf("32bit")!=-1));
+
+ var is_os2 = ((agt.indexOf("os/2")!=-1) ||
+ (navigator.appVersion.indexOf("OS/2")!=-1) ||
+ (agt.indexOf("ibm-webexplorer")!=-1));
+
+ var is_mac = (agt.indexOf("mac")!=-1);
+ var is_mac68k = (is_mac && ((agt.indexOf("68k")!=-1) ||
+ (agt.indexOf("68000")!=-1)));
+ var is_macppc = (is_mac && ((agt.indexOf("ppc")!=-1) ||
+ (agt.indexOf("powerpc")!=-1)));
+
+ var is_sun = (agt.indexOf("sunos")!=-1);
+ var is_sun4 = (agt.indexOf("sunos 4")!=-1);
+ var is_sun5 = (agt.indexOf("sunos 5")!=-1);
+ var is_suni86= (is_sun && (agt.indexOf("i86")!=-1));
+ var is_irix = (agt.indexOf("irix") !=-1); // SGI
+ var is_irix5 = (agt.indexOf("irix 5") !=-1);
+ var is_irix6 = ((agt.indexOf("irix 6") !=-1) || (agt.indexOf("irix6") !=-1));
+ var is_hpux = (agt.indexOf("hp-ux")!=-1);
+ var is_hpux9 = (is_hpux && (agt.indexOf("09.")!=-1));
+ var is_hpux10= (is_hpux && (agt.indexOf("10.")!=-1));
+ var is_aix = (agt.indexOf("aix") !=-1); // IBM
+ var is_aix1 = (agt.indexOf("aix 1") !=-1);
+ var is_aix2 = (agt.indexOf("aix 2") !=-1);
+ var is_aix3 = (agt.indexOf("aix 3") !=-1);
+ var is_aix4 = (agt.indexOf("aix 4") !=-1);
+ var is_linux = (agt.indexOf("inux")!=-1);
+ var is_sco = (agt.indexOf("sco")!=-1) || (agt.indexOf("unix_sv")!=-1);
+ var is_unixware = (agt.indexOf("unix_system_v")!=-1);
+ var is_mpras = (agt.indexOf("ncr")!=-1);
+ var is_reliant = (agt.indexOf("reliantunix")!=-1);
+ var is_dec = ((agt.indexOf("dec")!=-1) || (agt.indexOf("osf1")!=-1) ||
+ (agt.indexOf("dec_alpha")!=-1) || (agt.indexOf("alphaserver")!=-1) ||
+ (agt.indexOf("ultrix")!=-1) || (agt.indexOf("alphastation")!=-1));
+ var is_sinix = (agt.indexOf("sinix")!=-1);
+ var is_freebsd = (agt.indexOf("freebsd")!=-1);
+ var is_bsd = (agt.indexOf("bsd")!=-1);
+ var is_unix = ((agt.indexOf("x11")!=-1) || is_sun || is_irix || is_hpux ||
+ is_sco ||is_unixware || is_mpras || is_reliant ||
+ is_dec || is_sinix || is_aix || is_linux || is_bsd || is_freebsd);
+
+ var is_vms = ((agt.indexOf("vax")!=-1) || (agt.indexOf("openvms")!=-1));
+
+
+
+//--> end hide JavaScript
+</script>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<!-- if you use the following meta tags, uncomment them.
+ <META NAME="keywords" CONTENT="FASTLINK linkage analysis genetic mapping">
+ <META NAME="description" CONTENT="software to carry out genetic linkage analysis to hunt for disease genes.">
+-->
+ <link rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi.css">
+</head>
+
+
+<body bgcolor="#FFFFFF" background="http://www.ncbi.nlm.nih.gov/corehtml/bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+<!-- the header -->
+<table border="0" width="600" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+ <td width="360" class="head1" valign="BOTTOM"> <span class="H1">Genetic Analysis Software</span></td>
+
+<!-- COMMENTED out
+ <td width="100" valign="BOTTOM">Your Logo</td>
+END of COMMENT -->
+
+ </tr>
+</table>
+<!-- the quicklinks bar -->
+<table CLASS="TEXT" border="0" width="600" cellspacing="0" cellpadding="3" bgcolor="#000000">
+ <tr CLASS="TEXT" align="CENTER">
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/PubMed/" class="BAR">PubMed</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/Entrez/" class="BAR">Entrez</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/BLAST/" class="BAR">BLAST</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/omim/" class="BAR">OMIM</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html" class="BAR">Taxonomy</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/Structure/" class="BAR">Structure</a></td>
+ </tr>
+</table>
+<!-- the contents -->
+<table border="0" width="600" cellspacing="0" cellpadding="0">
+ <tr valign="TOP"> <!-- left column -->
+ <td width="125">
+ <img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="125" height="1" border="0">
+
+ <p>
+ <span class="GUTTER1">Downloads</span>
+ <br>
+ <br>
+ <a href="ftp://fastlink.nih.gov/pub/fastlink/fastlink.tar.Z" class="GUTTER2">FASTLINK package</a>
+ <br>
+ <br>
+ <a href="ftp://fastlink.nih.gov/pub/fastlink/mac/FASTLINK_executables.zip" class="GUTTER2">FASTLINK executables for Mac OS X</a>
+ <br>
+ <br>
+ <a href="ftp://fastlink.nih.gov/pub/fastlink/README" class="GUTTER2">README</a>
+ <br>
+ <br>
+ <a href="ftp://fastlink.nih.gov/pub/fastlink/README.updates" class="GUTTER2">README.updates</a>
+ <br>
+ <br>
+ <a href="ftp://fastlink.nih.gov/pub/fastlink/unknown.ps" class="GUTTER2">unknown.ps</a>
+ <br>
+ <br>
+ <a href="ftp://fastlink.nih.gov/pub/fastlink/loops.ps" class="GUTTER2">loops.ps</a>
+ </p>
+ <p> </p>
+ <a href="fastref.html" class="GUTTER1">References</a>
+ </p>
+ </td>
+ <!-- extra column to force things over the gif border -->
+ <td width="15"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="15" height="1" border="0"> </td>
+ <!-- right content column -->
+ <td width="310">
+<img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="310" height="1">
+ <p> </p>
+ <!-- title with bullet -->
+ <table border="0" width="460" cellspacing="2" cellpadding="0" bgcolor="#FFFFFF">
+ <tr>
+ <td width="7" bgcolor="#315399"> </td>
+ <td width="303" bgcolor="#CCCCFF" class="H3"> Overview</td>
+ </tr>
+ </table>
+
+ <p>
+ Genetic linkage analysis is a statistical technique used to map
+ genes and find the approximate location of disease genes.
+ There was a standard software package for genetic linkage
+ called LINKAGE. FASTLINK is a significantly modified and
+ improved version of the main programs of LINKAGE that
+ runs much faster sequentially, can run in parallel, allows
+ the user to recover gracefully from a computer crash, and
+ provides abundant new documentation. FASTLINK has been
+ used in over 1000 published genetic linkage studies.
+ </p>
+
+ <p>
+ Version 1.0 of FASTLINK was first distributed in May 1993.
+ We are now up to version 4.1P, first released in July 1999. You
+ can download the current version with all documentation as
+ well as some individual documentation files by following
+ the hyperlinks on the left-hand side of this page. When
+ you retrieve FASTLINK as a whole, you will get 1 file called
+ fastlink.tar.Z. To unpack the archive on a UNIX machine, issue
+ the commands
+ <pre>
+ uncompress fastlink.tar.Z
+ tar -xvf fastlink.tar
+ </pre>
+ Users who do not have access to <tt>uncompress</tt> and <tt>tar</tt>
+ equivalents can get the entire distribution piecemeal by ftp'ing to
+ the server fastlink.nih.gov, logging in as user <tt>anonymous</tt>,
+ and going to the directory <tt>pub/fastlink</tt>.
+ Start with the file <tt>README</tt>, which is available by a direct
+ hyperlink on the left to get a roadmap to all the documentation.
+ If you want to see whether a new version of FASTLINK contains
+ improvements that you want, look at the file README.updates, also
+ available by a single click on the left. Thanks to David Stockton
+ executables of the FASTLINK programs suitable for Macintosh OS X
+ are available either by clinking on a hyperlink on this page or
+ from the ftp site fastlink.nih.gov under directory
+ <tt>pub/fastlink/mac</tt>. Other files of interest to Macintosh
+ users are in that ftp directory.
+ </p>
+
+ <p>
+ The FASTLINK project is directed by
+ <A href="mailto:schaffer at helix.nih.gov">Alejandro Schäffer</A>.
+ Over the years, participants in developing FASTLINK and
+ providing customer service have included: Richa Agarwala (NIH)
+ Ann Becker (Technion), Robert Cottingham Jr.,
+ Alan Cox (Rice U.),
+ <A href="http://www.cs.rochester.edu/u/sandhya">Sandhya Dwarkadas</A> (now at U. Rochester),
+ Dan Geiger (Technion), Sandeep Gupta (now at Trilogy),
+ Christopher Hoelscher, Chris Hyams (now at Trilogy),
+ Ramana Idury (now at Kiva Genetics),
+ Peter Keleher (now at U. Maryland), K. Shriram (Rice U.)
+ Willy Zwaenepoel (Rice U.). I am also very grateful to
+ hundreds of users around the world for comments, questions,
+ suggestions, and bug reports, and most of all for being bold
+ enough to try some new software and stick with it.
+ </p>
+
+ <p>
+ The FASTLINK project has benefited from two interesting
+ concepts from computer systems. First, K. Shriram implemented
+ a checkpointing facility that allows the FASTLINK main programs
+ to recover gracefully from a crash of the underlying computer.
+ Stephen Rich (now at Wake Forest U.) gets the prize for the most
+ unusual usage of checkpoint/crash recovery. Just before moving
+ his workstation from Minnesota to North Carolina, he killed
+ an ongoing FASTLINK run, and shut down the computer. Once he
+ and the workstation got installed in North Carolina, he resumed
+ the run near where it left off and completed it successfully.
+ I have reused some of K. Shriram's checkpointing code in the
+ PSI-BLAST module of the widely used
+ <A href="http://www.ncbi.nlm.nih.gov/BLAST">BLAST</A>
+ package.
+ </p>
+
+ <p>
+ Starting with version 2.3P, the ilink, mlink, and linkmap
+ programs in FASTLINK can run in parallel. What is especially
+ surprising is that essentially the same code can run on
+ either shared-memory multiprocessors or on homogeneous
+ networks of uniprocessors. This feat is made possible by using
+ the <A href="http://www.cs.rice.edu/~willy/TreadMarks/overview.html"> TreadMarks
+</A>
+ distributed shared memory system developed at Rice University.
+ </p>
+
+ <p>
+ FASTLINK comes with substantial documentation. Most of
+ the documentation files are in ASCII text. Two of the more
+ popular documents that are in PostScript are:
+ <A href="unknown.html"> The Mystery of (the) Unknown</A>,
+ which explains the preprocessor program unknown, and
+ <A href= "loops.html"> Loops in FASTLINK </A>. You can download
+ PostScript versions by clicking on the hyperlinks to the left
+ or read the documents one page at a time by clicking on the
+ hyperlinks in this paragraph.
+ Thanks to many users and especially the student participants
+ on the FASTLINK projects who kept asking questions that
+ deserved clear and written answers for everyone's benefit.
+ </p>
+
+ <p>
+ To promote better understanding of how to do simple
+ linkage analyses, I teach a class called
+ <A href= "http://bimas.cit.nih.gov/linkage/index.html"> "Cookbook Linkage Analysis, Ab Initio" </A>.
+ Follow the hyperlink in this paragraph
+ to get to a page that lets you link to the course overheads
+ and 11 recipes for different aspects of linkage analysis.
+ Thanks to Jim Tomlin for putting the course materials on the Web.
+ </p>
+
+ <p>
+I maintain a mailing list of FASTLINK users, used mostly to
+announce new versions, updates, and bug fixes. If you have retrieved the
+code and would like to be on the mailing list, send me e-mail at
+<a href="mailto:schaffer at helix.nih.gov">schaffer at helix.nih.gov</a>.
+ </p>
+
+
+ <p> </p>
+ </td>
+ </tr>
+</table>
+<!-- end of content -->
+
+
+
+ <table bgcolor="#CCCCFF" border="0" cellpadding="0" cellspacing="0" width=594>
+ <tr align="CENTER">
+ <td width="99"><a href="http://www.ncbi.nlm.nih.gov/Web/NCBI/address.list.html" class="HELPBAR">[Help]</a></td>
+ <td width="99"><a href="http://www.ncbi.nlm.nih.gov/corehtml/search.html" class="HELPBAR">[Search]</a></td>
+ <td width="99"><a href="http://www.ncbi.nlm.nih.gov/BLAST/" class="HELPBAR"> </a></td>
+ <td width="99"><a href="http://www.ncbi.nlm.nih.gov/omim/" class="HELPBAR"> </a></td>
+ <td width="99">
+ <a href="http://www.nlm.nih.gov" class="HELPBAR">[NLM</a>
+ <a href="http://www.nih.gov" class="HELPBAR">NIH]</a>
+ </td>
+ <td width="99"><a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html" class="HELPBAR">[Disclaimer]</a></td>
+ </tr>
+ </table>
+
+
+</body>
+</html>
Added: trunk/packages/fastlink/trunk/debian/fastlink.install
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink.install (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink.install 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,6 @@
+4.1P/src/lodscore usr/bin
+4.1P/src/ilink usr/bin
+4.1P/src/linkmap usr/bin
+4.1P/src/mlink usr/bin
+4.1P/src/unknown usr/bin
+debian/*.desktop usr/share/applications
Added: trunk/packages/fastlink/trunk/debian/fastlink.manpages
===================================================================
--- trunk/packages/fastlink/trunk/debian/fastlink.manpages (rev 0)
+++ trunk/packages/fastlink/trunk/debian/fastlink.manpages 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,5 @@
+debian/ilink.1
+debian/linkmap.1
+debian/lodscore.1
+debian/mlink.1
+debian/unknown.1
Added: trunk/packages/fastlink/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/fastlink/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/fastlink/trunk/debian/get-orig-source 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,28 @@
+#!/bin/sh -e
+
+NAME=fastlink
+UPSTREAMTAR="$NAME".tar.Z
+MAINVERSION="4.1P"
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+if [ ! -f "$UPSTREAMTAR" ] ; then
+ wget ftp://fastlink.nih.gov/pub/fastlink/fastlink.tar.Z
+fi
+tar -xzf "$UPSTREAMTAR"
+
+PATCHVERSION=`grep -v "^ " fastlink/README.updates | tail -n 1 | sed 's/^\([0-9a-z]\+\)\..*/\1/'`
+UPSTREAMVERSION="${MAINVERSION}-fix${PATCHVERSION}"
+UPSTREAMDIR="{$NAME}-${UPSTREAMVERSION}"
+
+mv "$NAME" "$UPSTREAMDIR"
+# Remove useless files
+rm -rf "$UPSTREAMDIR"/aix \
+ "$UPSTREAMDIR"/4.1P/alphavms \
+ "$UPSTREAMDIR"/4.1P/irix \
+ "$UPSTREAMDIR"/4.1P/vaxvms
+
+GZIP=-9 tar -czf "$NAME"_"$UPSTREAMVERSION".orig.tar.gz "$UPSTREAMDIR"
+
+rm -rf "$UPSTREAMDIR"
Property changes on: trunk/packages/fastlink/trunk/debian/get-orig-source
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/fastlink/trunk/debian/ilink.1
===================================================================
--- trunk/packages/fastlink/trunk/debian/ilink.1 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/ilink.1 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,58 @@
+.TH ILINK 1 "April 15, 2003"
+.SH NAME
+ilink \- GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions
+.SH SYNOPSIS
+.B ilink
+.RI [ options ] " ipedfile.dat pedfile.dat"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B ilink
+command. In fact this is a very raw intend to provide a manpage because
+the Debian GNU/Linux distribution requires each program to have a manpage.
+Any enhancement would be greatly apreciated.
+.PP
+\fBilink\fP is part of the \fBfastlink\fP software package.
+.PP
+ILINK uses the GEMINI optimization procedure to find a locally optimal value of
+the theta vector of recombination fractions. If you use the default scripts
+produced by lcp, your initial guess for theta is .1 in every dimension.
+GEMINI evaluates each theta by its likelihood, seeking to find theta vectors
+that have a higher pedigree likelihood.
+.PP
+The GEMINI procedure has multiple iterations. Each iteration corresponds to one
+line of output. Each iteration includes multiple likelihood function evaluations.
+Each iteration has two phases. In Phase I GEMINI seeks to improve the current best
+theta. In Phase II, GEMINI estimates the gradient of the likelihood with respect
+to the current best theta vector. In the first iteration, Phase I only evaluates
+the likelihood at the initial candidate theta.
+
+When ILINK prints out a line such as: maxcensor can be reduced to -32767, it has
+completed the first likelihood function evaluation. On long runs, this fact can be
+used to estimate running time. A reasonable rough estimate for the number of
+function evaluations is 10*(number of dimensions of theta vector). The number
+of dimensions of the theta vector is one fewer than the number of loci in most
+cases. If maletheta and femaletheta are allowed to differ (sexdif is set to 1),
+then the number of dimensions doubles to 2 * (number of loci - 1). Estimating
+other parameters (with fitmodel set to true) can also increase the number of dimensions.
+
+To learn more about
+.B ilink
+it might be useful to read the file
+.I /usr/share/doc/fastlink/README.ILINK
+if you have a Debian GNU/Linux system.
+
+.SH OPTIONS
+There might be options but I did not found any information about them.
+Please foreward any information about them to <tille at debian.org>
+.SH SEE ALSO
+linkmap(1), lodscore(1), mlink(1), unknown(1).
+.br
+.SH Word-Wide-Web:
+http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+.SH AUTHOR:
+.I Alejandro Schaeffer
+<schaffer at helix.nih.gov>
+and others
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/fastlink/trunk/debian/ilink.desktop
===================================================================
--- trunk/packages/fastlink/trunk/debian/ilink.desktop (rev 0)
+++ trunk/packages/fastlink/trunk/debian/ilink.desktop 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Exec=ilink
+Name=ilink
+GenericName=Fastlink GEMINI optimization
+GenericName[en]=Fastlink GEMINI optimization
+Comment=GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions
+Comment[en]=GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions
+Type=Application
+Categories=Biology;Science;Education;
Added: trunk/packages/fastlink/trunk/debian/linkage.5
===================================================================
--- trunk/packages/fastlink/trunk/debian/linkage.5 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/linkage.5 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,210 @@
+.TH LINKAGE 5 "April 22, 2003"
+.SH NAME
+LINKAGE \- general information about LINKAGE's file formats
+.SH "DESCRIPTION"
+The input data consist of pedigree and genotypic information contained
+in one file, and locus descriptions, recombination rates and locus
+order contained in a second file. These files are entitled
+.BR PEDFILE (5)
+and
+.BR DATAFILE (5),
+respectivly.
+.SS "Phenotypes and Genotypes"
+To understand the format of the input files, you must know what kinds
+of phenotypic data can be interpreted by the LINKAGE
+programs. Phenotype data can be one of the following types:
+.IP \(bu 5
+.BR "Numbered alleles".
+These are codominant alleles at a single locus. The numbers run consecutively from 1 to the maximum number of alleles observed. The phenotype consists of two allele numbers corresponding to a genotype. An unknown genotype is coded as 0 0.
+.IP \(bu 5
+.BR "Binary factors".
+In this coding scheme a series of binary codes (1 or 0) indicates the presence or absence of a phenotype factor. This system is useful for describing either codominant or recessive/dominant systems. The phenotype is entered as a binary string.
+.IP \(bu 5
+.BR "Affection status".
+The presence or absence of disease (or other qualitative phenotypes) is described by a numbered code. A risk or liability class can also be included as a separate numeric code.
+.IP \(bu 5
+.BR "Quantitative traits".
+One or more quantitative measurements can be used as a phenotype description.
+.PP
+The phenotypic codes for each of these types of data are described in more detail below.
+.TP
+.BR "NOTE":
+The present version of LINKAGE does not allow mixtures of affection status and quantitative variables, except in the case of sex-linked traits as described below. A future version will incorporate a modification allowing such mixtures for autosomal data.
+.SS "Numbered Allies"
+Numbering alleles is the simplest way to code codominant marker
+data. A homozygote is indicated by repeating the allele number; thus 1
+2 indicates that the alleles are 1 and 2 (a heterozygotea) while 1 1
+indicates the alleles are 1 and 1 (a homozygote). An unknown genotype
+is coded as 0 0. For sex-linked loci, males have a single allele. With
+the allele 1, for example, the phenotype can be coded 1 0 or 1 1.
+.SS "Binary Factors"
+Binary factors (sometimes called "factor-union" notation) can also
+represent phenotypes for codominant marker data, but this coding is
+most useful with recessive alleles or with complex systems such as Rh,
+ABO, and Gm. Each allele is assigned a set of properties, called
+factors, in such a way that all phenotypes can be specified as the
+union of two allele sets.
+
+For codominant loci, each allele can be associated with one factor. If
+n alleles are present, the ith allele is represented by a series of n
+binary codes with a 0 in all locations, except in the ith position,
+which contains a 1. For example, in a two allele system the allelic
+codes are:
+
+.TS
+center;
+n1 n1 l.
+1 0 (allele 1)
+0 1 (allele 2)
+.TE
+
+
+The three possible phenotypes are:
+
+.TS
+center;
+n1 n1 l.
+1 0 (union of alleles 1 and 1)
+1 1 (union of alleles 1 and 2)
+0 1 (union of alleles 2 and 2)
+.TE
+
+
+An unknown phenotype is coded as 0 0. Spaces between the codes are
+very important; they must be included when entering the phenotypes
+into the pedigree file as described below.
+
+A locus with three codominant alleles is coded as:
+
+.TS
+center;
+n1 n1 n1 l.
+1 0 0 (allele 1)
+0 1 0 (allele 2)
+0 0 1 (allele 3)
+.TE
+
+
+The six possible phenotypes are:
+
+.TS
+center;
+n1 n1 n1 l.
+1 0 0 (union of alleles 1 and 1)
+1 1 0 (union of alleles 1 and 2)
+1 0 1 (union of alleles 1 and 3)
+0 1 0 (union of alleles 2 and 2)
+0 1 1 (union of alleles 2 and 3)
+0 0 1 (union of alleles 3 and 3)
+.TE
+
+
+and an unknown phenotype is 0 0 0.
+
+The advantage of the binary factor coding scheme is evident when a
+recessive disease gene is under study. To code such a system, we could
+indicate the normal gene by the presence of a single factor (1) and
+the disease gene by the absence of this factor (0). The phenotype 1
+(unaffected) now corresponds to two possible genotypes, either the
+union of allele 1 and allele 1 (noncarrier) or the union of allele 1
+and allele 0 (carrier).
+
+This simple coding is usually not sufficient because both homozygote
+recessive and unknown phenotypes are coded as 0. To account for this,
+we introduce a second factor for which a 1 indicates that the
+phenotype is known, and a 0 that the phenotype is unknown. The allelic
+codes are:
+
+.TS
+center;
+n1 n1 l.
+1 1 (allele 1)
+0 1 (allele 2)
+.TE
+
+and the possible phenotypes are:
+
+.TS
+center;
+n1 n1 l.
+1 1 (union of alleles 1 and 1, or alleles 1 and 2)
+0 1 (union of alleles 2 and 2)
+0 0 (unknown)
+.TE
+
+.SS "Affected Status"
+"Affection status" refers to the presence or absence of disease. The
+programs assume that an affected individual will have the phenotype
+code "2" and that an unknown individual will have the code "0." By
+convention, "1" is used to designate unaffected status (in fact, this
+code can be any integer value other than 0 and 2). If necessary, the
+unknown and affected codes can be changed in the program code, and the
+programs recompiled.
+
+For an "affection-status" locus, each genotype has an associated
+penetrance; this is the probability that an individual with a
+particular genotype will be affected. Penetrance can also be defined
+as a function of liability classes. In this case, one penetrance is
+given for each genotype in each liability class. The classes are
+numbered sequentially starting from 1. With two or more liability
+classes, the phenotype is the affection status plus the class
+number. When a single affection status class is defined, the class
+number is not included as part of the phenotype.
+
+With sex-linked traits, different penetrances must be given for
+females and males. One penetrance in males is specified for each
+allele in each liability class.
+.SS "Quantitative Variables"
+Phenotypic information is sometimes presented in the form of
+quantitative measurements, e.g. creatine kinase for carrier detection
+in Duchenne muscular dystrophy. The phenotype is then the quantitative
+value. Unknown phenotypes are entered as 0.0. (The code for unknown
+quantitative values is a program constant that can be changed.) The
+genotypic means, the variance of the trait in homozygotes, and the
+ratio of the variances in heterozygotes and homozygotes must be
+specified.
+
+If several traits are measured for the same locus, the phenotype is
+the list of all the variables. A single value of 0.0 in the list is
+interpreted as an unknown phenotype. The means must be given for each
+variable as a function of genotype, along with the variance-covariance
+matrix. The variance matrices for homozygotes and heterozygotes can
+differ by a constant factor.
+
+For sex-linked traits it is assumed that males will have an
+affection-status variable rather than a quantitative value. If several
+variables have been measured (ntrait), a male phenotype consists of
+affection status followed by ntrait-1 arbitrary entries (for example,
+zeros). The present version of the programs supports only one
+affection status class, with full penetrance of the disease allele for
+sex-linked traits.
+
+.SH NOTES
+The information contained herein was gleaned, often-times verbatim,
+from
+.UR http://linkage.rockefeller.edu/soft/linkage/
+the LINKAGE User's Guide
+.UE
+on the web by kind permission of Jurg Ott, Ph.D.
+
+.SH AUTHORS
+Mark Lathrop and Jurg Ott.
+.PP
+This manual page was written by Elizabeth Barham
+<lizzy at soggytrousers.net> for the Debian GNU/Linux distribution.
+
+.SH WORLD-WIDE-WEB
+.UR http://linkage.rockefeller.edu/soft/linkage/
+http://linkage.rockefeller.edu/soft/linkage/
+.UE
+
+.SH SEE ALSO
+.BR DATAFILE (5),
+.BR PEDFILE (5),
+.BR ilink (1),
+.BR linkmap (1),
+.BR lodscore (1),
+.BR mlink (1),
+and
+.BR unknown (1).
+
Added: trunk/packages/fastlink/trunk/debian/linkmap.1
===================================================================
--- trunk/packages/fastlink/trunk/debian/linkmap.1 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/linkmap.1 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,29 @@
+.TH LINKMAP 1 "April 15, 2003"
+.SH NAME
+linkmap \- calculates location scores of one locus against a fixed map of other loci
+.SH SYNOPSIS
+.B linkmap
+.RI [ options ] " ipedfile.dat pedfile.dat"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B linkmap
+command. In fact this is a very raw intend to provide a manpage because
+the Debian GNU/Linux distribution requires each program to have a manpage.
+Any enhancement would be greatly apreciated.
+.PP
+\fBlinkmap\fP is part of the \fBfastlink\fP software package.
+.SH OPTIONS
+There might be options but I did not found any information about them.
+Please foreward any information about them to <tille at debian.org>
+.SH SEE ALSO
+ilink(1), lodscore(1), mlink(1), unknown(1).
+.br
+.SH Word-Wide-Web:
+http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+.SH AUTHOR:
+.I Alejandro Schaeffer
+<schaffer at helix.nih.gov>
+and others
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/fastlink/trunk/debian/linkmap.desktop
===================================================================
--- trunk/packages/fastlink/trunk/debian/linkmap.desktop (rev 0)
+++ trunk/packages/fastlink/trunk/debian/linkmap.desktop 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Exec=linkmap
+Name=linkmap
+GenericName=Fastlink location scores
+GenericName[en]=Fastlink location scores
+Comment=Calculates location scores of one locus against a fixed map of other loci
+Comment[en]=Calculates location scores of one locus against a fixed map of other loci
+Type=Application
+Categories=Biology;Science;Education;
Added: trunk/packages/fastlink/trunk/debian/lodscore.1
===================================================================
--- trunk/packages/fastlink/trunk/debian/lodscore.1 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/lodscore.1 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,40 @@
+.TH LODSCORE 1 "April 15, 2003"
+.SH NAME
+lodscore \- compares likelihoods at locally optimal theta
+.SH SYNOPSIS
+.B lodscore
+.RI [ options ] " ipedfile.dat pedfile.dat"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B lodscore
+command. In fact this is a very raw intend to provide a manpage because
+the Debian GNU/Linux distribution requires each program to have a manpage.
+Any enhancement would be greatly apreciated.
+.PP
+\fBlodscore\fP is part of the \fBfastlink\fP software package.
+.PP
+.B Lodscore
+compares -2log(likelihood)
+at the locally optimal theta to -2log(likelihood) at a theta that is
+.5 in every component (i.e. each locus unlinked to all the rest).
+In LINKAGE ILINK more likelihood function evaluations are done after
+the last printed iteration line, but these likelihood function
+evaluations are unnecessary (see paper2.ps from the
+.I fastlink-doc
+Debian package for more details).
+
+.SH OPTIONS
+There might be options but I did not found any information about them.
+Please foreward any information about them to <tille at debian.org>
+.SH SEE ALSO
+ilink(1), linkmap(1), mlink(1), unknown(1).
+.br
+.SH Word-Wide-Web:
+http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+.SH AUTHOR:
+.I Alejandro Schaeffer
+<schaffer at helix.nih.gov>
+and others
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/fastlink/trunk/debian/lodscore.desktop
===================================================================
--- trunk/packages/fastlink/trunk/debian/lodscore.desktop (rev 0)
+++ trunk/packages/fastlink/trunk/debian/lodscore.desktop 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Exec=lodscore
+Name=lodscore
+GenericName=Fastlink compare likelihoods
+GenericName[en]=Fastlink compare likelihoods
+Comment=Compares likelihoods at locally optimal theta
+Comment[en]=Compares likelihoods at locally optimal theta
+Type=Application
+Categories=Biology;Science;Education;
Added: trunk/packages/fastlink/trunk/debian/mlink.1
===================================================================
--- trunk/packages/fastlink/trunk/debian/mlink.1 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/mlink.1 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,29 @@
+.TH MLINK 1 "April 15, 2003"
+.SH NAME
+mlink \- calculates lod scores and risk with two of more loci
+.SH SYNOPSIS
+.B mlink
+.RI [ options ] " ipedfile.dat pedfile.dat"
+.SH DESCRIPTION
+This manual page documents briefly the
+.B mlink
+command. In fact this is a very raw intend to provide a manpage because
+the Debian GNU/Linux distribution requires each program to have a manpage.
+Any enhancement would be greatly apreciated.
+.PP
+\fBmlink\fP is part of the \fBfastlink\fP software package.
+.SH OPTIONS
+There might be options but I did not found any information about them.
+Please foreward any information about them to <tille at debian.org>
+.SH SEE ALSO
+ilink(1), linkmap(1), lodscore(1), unknown(1).
+.br
+.SH Word-Wide-Web:
+http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+.SH AUTHOR:
+.I Alejandro Schaeffer
+<schaffer at helix.nih.gov>
+and others
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/fastlink/trunk/debian/mlink.desktop
===================================================================
--- trunk/packages/fastlink/trunk/debian/mlink.desktop (rev 0)
+++ trunk/packages/fastlink/trunk/debian/mlink.desktop 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Exec=mlink
+Name=mlink
+GenericName=Fastlink lod scores
+GenericName[en]=Fastlink lod scores
+Comment=Calculate lod scores and risk with two of more loci
+Comment[en]=Calculate lod scores and risk with two of more loci
+Type=Application
+Categories=Biology;Science;Education;
Added: trunk/packages/fastlink/trunk/debian/pedfile.5
===================================================================
--- trunk/packages/fastlink/trunk/debian/pedfile.5 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/pedfile.5 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,279 @@
+.TH PEDFILE 5 "April 22, 2003"
+.SH NAME
+PEDFILE \- LINKAGE's PEDFILE, Pedigree Information
+.SH DESCRIPTION
+In addition to phenotypes and description of loci, the LINKAGE
+programs require pedigree information in order to traverse the
+pedigree when calculating the likelihood. The input must contain the
+following information for each individual:
+.IP \(bu 5
+a pedigree number
+.IP \(bu 5
+an individual identification number, or id
+.IP \(bu 5
+father's id number
+.IP \(bu 5
+mother's id number
+.IP \(bu 5
+first offspring id number
+.IP \(bu 5
+next paternal sibling id number
+.IP \(bu 5
+next maternal sibling id number
+.IP \(bu 5
+sex
+.IP \(bu 5
+"proband status"
+.PP
+The first offspring can be any of an individual's children, but the
+next sib id's for the offspring will be constrained by this
+choice. The next-paternal-sibling and next-maternal-sibling numbers,
+along with first-offspring number, provide a set of pointers to pass
+from one child to the next. The first offspring of the father is any
+of his children; the next paternal sib of the first offspring is any
+other of his children, etc. The entry for the next paternal sib of the
+last child is "0". Similar pointers are made for the mother's
+children. For full-sibs, it is convenient to make id's for the next
+maternal and next paternal siblings identical, but when one or both
+parents have children from different marriages, at least some will
+have different values.
+
+Father and mother id's are 0 for founders, or other members of the
+pedigree for whom information on parents is absent. Otherwise, both
+parents must be present in the pedigree even if one is unknown. If one
+parent is unknown, an id number must still be created, and a record
+for the fictitious parent must appear in the pedigree file.
+
+The "proband" refers to a starting individual for linkage calculations
+(indicated by a 1 in the proband field). The choice of the proband is
+not necessarily related to the ascertainment of the pedigree; indeed,
+it is usually more efficient to calculate from a founding ancestor
+rather than from the true proband. Risks are also calculated for the
+person designated as the proband. Other individuals should have a 0 in
+the proband field, except in pedigrees containing inbreeding or
+marriage loops as discussed in section 2.8. If no proband is
+designated, the first individual encountered for a pedigree will be
+used as a starting point for the calculation.
+
+The sex field is coded 1 for males and 2 for females. These default
+values can be changed by modifying a program constant.
+
+The creation of the first offspring, next maternal sib and next
+paternal sib pointers is done automatically by the program MAKEPED
+(not covered in this document). The input to the MAKEPED program is a
+file with individual records containing the pedigree number, id
+number, father id, mother id, sex and phenotypic data. The phenotypic
+data are coded as discussed in
+.BR LINKAGE (5)
+and in the following examples. The MAKEPED program also allows
+automatic selection of probands for efficient likelihood calculations.
+
+.SH EXAMPLE
+Consider the pedigree shown in Figure 1. Data on three loci are
+presented: one disease locus and two marker loci. An "a" below an
+individual stands for "affected," and "u" stands for unknown. The
+first marker locus has three alleles present in the pedigree, while
+the second has two alleles present.
+
+ [1]--.--(2)
+ a |
+ 22 | 12
+ 12 | 12
+ Figure 1 |
+ .------+------.
+ | | |
+ (6)--.--[3] [4] (5)
+ | a
+ 13 | 12
+ 12 | 22
+ |
+ .-------.
+ | |
+ [7] (8)--.--(10)
+ a |
+ 13 u | 12
+ 22 u | 12
+ |
+ (9)
+ a
+ 11
+ 12
+
+The input PEDFILE can take the following form:
+
+.TS
+center;
+n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 l l.
+1 1 0 0 3 0 0 1 1 2 0 1 0 1 1 Ped: 1 Per: 1
+1 2 0 0 3 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 2
+1 3 1 2 7 4 4 1 0 2 1 1 0 0 1 Ped: 1 Per: 3
+1 4 1 2 0 5 5 1 0 1 0 1 0 1 1 Ped: 1 Per: 4
+1 5 1 2 0 0 0 2 0 2 1 1 0 0 1 Ped: 1 Per: 5
+1 6 0 0 7 0 0 2 0 1 1 0 1 1 1 Ped: 1 Per: 6
+1 7 3 6 0 8 8 1 0 2 1 0 1 0 1 Ped: 1 Per: 7
+1 8 3 6 9 0 0 1 0 1 0 0 0 0 0 Ped: 1 Per: 8
+1 9 8 10 0 0 0 2 0 2 1 0 0 1 1 Ped: 1 Per: 9
+1 10 0 0 9 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 10
+.TE
+
+The PEDFILE has been produced from an input file by the MAKEPED
+program. The comments at the end of each record indicate original
+pedigree and id codes. The first entry in each record is followed by
+the pedigree number, id number, five pedigree pointers (father id,
+mother id, first offspring id, next paternal sib id, next maternal sib
+id), sex, proband, disease status, and marker loci coded as binary
+factors. Comparison with the original pedigree will reveal the coding
+scheme. Individual 1 has been chosen as the "proband;" as this is the
+first individual of this pedigree encountered in the file, the entry
+in the proband field is optional.
+
+Now consider the same pedigree extended to include some half sibs
+(Figure 2).
+
+ [1]--.--(2)
+ a |
+ Figure 2 22 | 12
+ 12 | 12
+ |
+ .------+------.
+ | | |
+ (6)--.--[3] [4] (5)
+ | a a
+ 13 | 12 22 12
+ 12 | 22 12 22
+ |
+ .-------------------------.
+ | |
+ (11)--.--[7]--.--(12)--.--[13] (8)--.--(10)
+ | a | | |
+ u | 13 | 12 | u u | 12
+ u | 22 | 12 | u u | 12
+ | | | |
+ (14) (15) (16) (9)
+ a
+ 13 13 11 11
+ 12 12 12 12
+
+The MAKEPED program produces the following file for this pedigree (figure 2):
+
+.TS
+center;
+n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 l l.
+1 1 0 0 3 0 0 1 1 2 0 1 0 1 1 Ped: 1 Per: 1
+1 2 0 0 3 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 2
+1 3 1 2 7 4 4 1 0 2 1 1 0 0 1 Ped: 1 Per: 3
+1 4 1 2 0 5 5 1 0 1 0 1 0 1 1 Ped: 1 Per: 4
+1 5 1 2 0 0 0 2 0 2 1 1 0 0 1 Ped: 1 Per: 5
+1 6 0 0 7 0 0 2 0 1 1 0 1 1 1 Ped: 1 Per: 6
+1 7 3 6 14 8 8 1 0 2 1 0 1 0 1 Ped: 1 Per: 7
+1 8 3 6 9 0 0 1 0 1 0 0 0 0 0 Ped: 1 Per: 8
+1 9 8 10 0 0 0 2 0 2 1 0 0 1 1 Ped: 1 Per: 9
+1 10 0 0 9 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 10
+1 11 0 0 14 0 0 2 0 1 0 0 0 0 0 Ped: 1 Per: 11
+1 12 0 0 15 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 12
+1 13 0 0 16 0 0 1 0 1 0 0 0 0 0 Ped: 1 Per: 13
+1 14 7 11 0 15 0 2 0 1 1 0 1 1 1 Ped: 1 Per: 14
+1 15 7 12 0 0 16 2 0 1 1 0 1 1 1 Ped: 1 Per: 15
+1 16 13 12 0 0 0 2 0 1 1 0 0 1 1 Ped: 1 Per: 16
+.TE
+
+The following data refer to a larger pedigree, taken from a coronary
+heart disease study, in PEDFILE form:
+.TS
+center;
+n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 l l.
+1 1 0 0 3 0 0 2 0 2 3 0 0 0.00 Ped: 1 Per: 1
+1 2 0 0 3 0 0 1 1 2 3 0 0 0.00 Ped: 1 Per: 2
+1 3 2 1 7 5 5 1 0 2 2 0 0 0.00 Ped: 1 Per: 3
+1 4 0 0 7 0 0 2 0 1 2 0 0 0.00 Ped: 1 Per: 4
+1 5 2 1 21 0 0 2 0 1 3 0 1 22.70 Ped: 1 Per: 5
+1 6 0 0 21 0 0 1 0 2 3 0 0 0.00 Ped: 1 Per: 6
+1 7 3 4 26 9 9 1 0 2 2 0 0 0.00 Ped: 1 Per: 7
+1 8 0 0 26 0 0 2 0 1 2 0 1 9.20 Ped: 1 Per: 8
+1 9 3 4 31 11 11 1 0 2 2 1 1 24.30 Ped: 1 Per: 9
+1 10 0 0 31 0 0 2 0 1 2 1 0 9.30 Ped: 1 Per: 10
+1 11 3 4 0 12 12 1 0 2 2 1 1 23.90 Ped: 1 Per: 11
+1 12 3 4 34 14 14 1 0 2 2 1 1 20.70 Ped: 1 Per: 12
+1 13 0 0 34 0 0 2 0 1 2 1 0 14.50 Ped: 1 Per: 13
+1 14 3 4 0 15 15 2 0 1 2 1 0 2.10 Ped: 1 Per: 14
+1 15 3 4 40 17 17 1 0 2 2 0 0 0.00 Ped: 1 Per: 15
+1 16 0 0 40 0 0 2 0 1 2 1 1 9.80 Ped: 1 Per: 16
+1 17 3 4 43 19 19 1 0 2 2 0 0 0.00 Ped: 1 Per: 17
+1 18 0 0 43 0 0 2 0 1 2 1 0 11.50 Ped: 1 Per: 18
+1 19 3 4 0 0 0 1 0 1 2 1 0 9.20 Ped: 1 Per: 19
+1 20 0 0 47 0 0 2 0 0 1 0 0 0.00 Ped: 1 Per: 20
+1 21 6 5 47 22 22 1 0 2 2 0 0 0.00 Ped: 1 Per: 21
+1 22 6 5 48 24 24 1 0 2 2 0 0 0.00 Ped: 1 Per: 22
+1 23 0 0 48 0 0 2 0 1 2 1 0 13.40 Ped: 1 Per: 23
+1 24 6 5 0 25 25 2 0 1 2 1 1 10.40 Ped: 1 Per: 24
+1 25 6 5 0 0 0 2 0 1 2 1 1 9.90 Ped: 1 Per: 25
+1 26 7 8 0 27 27 2 0 1 2 1 1 16.80 Ped: 1 Per: 26
+1 27 7 8 53 29 29 2 0 1 2 0 1 30.10 Ped: 1 Per: 27
+1 28 0 0 53 0 0 1 0 1 2 1 0 6.90 Ped: 1 Per: 28
+1 29 7 8 56 0 0 2 0 1 2 1 1 15.40 Ped: 1 Per: 29
+1 30 0 0 56 0 0 1 0 1 2 1 0 14.30 Ped: 1 Per: 30
+1 31 9 10 0 32 32 2 0 1 1 1 0 6.80 Ped: 1 Per: 31
+1 32 9 10 0 33 33 1 0 1 1 1 0 5.60 Ped: 1 Per: 32
+1 33 9 10 0 0 0 2 0 1 1 1 1 31.60 Ped: 1 Per: 33
+1 34 12 13 0 35 35 1 0 1 1 1 0 19.40 Ped: 1 Per: 34
+1 35 12 13 0 36 36 2 0 1 1 1 1 41.70 Ped: 1 Per: 35
+1 36 12 13 0 37 37 1 0 1 1 1 0 20.50 Ped: 1 Per: 36
+1 37 12 13 0 38 38 1 0 1 1 1 1 28.40 Ped: 1 Per: 37
+1 38 12 13 0 39 39 2 0 1 1 1 0 11.50 Ped: 1 Per: 38
+1 39 12 13 0 0 0 2 0 1 1 1 0 21.00 Ped: 1 Per: 39
+1 40 15 16 0 41 41 2 0 1 1 1 0 10.50 Ped: 1 Per: 40
+1 41 15 16 0 0 0 2 0 1 1 1 0 12.60 Ped: 1 Per: 41
+1 42 0 0 52 0 0 1 0 1 1 1 0 11.20 Ped: 1 Per: 42
+1 43 17 18 52 44 44 2 0 1 1 1 1 37.20 Ped: 1 Per: 43
+1 44 17 18 0 45 45 2 0 1 1 1 0 10.10 Ped: 1 Per: 44
+1 45 17 18 0 46 46 1 0 1 1 1 1 34.90 Ped: 1 Per: 45
+1 46 17 18 0 0 0 1 0 1 1 1 1 25.30 Ped: 1 Per: 46
+1 47 21 20 0 0 0 2 0 1 1 1 1 47.90 Ped: 1 Per: 47
+1 48 22 23 0 50 50 2 0 1 1 1 0 14.00 Ped: 1 Per: 48
+1 49 0 0 51 0 0 1 0 0 1 0 0 0.00 Ped: 1 Per: 49
+1 50 22 23 51 0 0 2 0 1 2 1 1 55.30 Ped: 1 Per: 50
+1 51 49 50 0 0 0 2 0 1 1 1 0 13.60 Ped: 1 Per: 51
+1 52 42 43 0 0 0 2 0 1 1 1 0 12.50 Ped: 1 Per: 52
+1 53 28 27 0 54 54 1 0 1 1 1 1 37.50 Ped: 1 Per: 53
+1 54 28 27 0 55 55 1 0 1 1 1 1 14.70 Ped: 1 Per: 54
+1 55 28 27 0 0 0 2 0 1 1 1 1 29.90 Ped: 1 Per: 55
+1 56 30 29 0 57 57 1 0 1 1 1 0 5.70 Ped: 1 Per: 56
+1 57 30 29 0 0 0 2 0 1 1 1 0 8.20 Ped: 1 Per: 57
+.TE
+
+Here, three loci are represented. The first is an affection status
+locus (coronary disease symptoms) with three liability classes (ages
+0-20, 20-40, and greater than 40); the second is a binary factor locus
+(LDL receptor polymorphism), and the third is a quantitative variable
+(age adjusted LDL cholesterol levels). Individuals with unknown
+affection status are assigned to the first liability class in this
+example, but the results would be the same irrespective of this
+assignment.
+.SH NOTES
+The information contained herein was gleaned, often-times verbatim,
+from
+.UR http://linkage.rockefeller.edu/soft/linkage/
+the LINKAGE User's Guide
+.UE
+on the web by kind permission of Jurg Ott, Ph.D.
+
+.SH AUTHORS
+Mark Lathrop and Jurg Ott.
+.PP
+This manual page was written by Elizabeth Barham
+<lizzy at soggytrousers.net> for the Debian GNU/Linux distribution.
+
+.SH WORLD-WIDE-WEB
+.UR http://linkage.rockefeller.edu/soft/linkage/
+http://linkage.rockefeller.edu/soft/linkage/
+.UE
+
+.SH SEE ALSO
+.BR LINKAGE (5),
+.BR DATAFILE (5),
+.BR ilink (1),
+.BR linkmap (1),
+.BR lodscore (1),
+.BR mlink (1),
+and
+.BR unknown (1).
Added: trunk/packages/fastlink/trunk/debian/rules
===================================================================
--- trunk/packages/fastlink/trunk/debian/rules (rev 0)
+++ trunk/packages/fastlink/trunk/debian/rules 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,18 @@
+#!/usr/bin/make -f
+# debian/rules for fastlink using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+DEB_AUTO_UPDATE_DEBIAN_CONTROL := yes
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+clean::
+ cd 4.1P/src; make allclean
+
+# Use makefile in subdir
+DEB_MAKE_INVOKE = cd 4.1P/src; $(DEB_MAKE_ENVVARS) make $(if $(DEB_MAKE_MAKEFILE), -f $(DEB_MAKE_MAKEFILE),) -C $(DEB_BUILDDIR) CFLAGS=$(if $(CFLAGS_$(cdbs_curpkg)),"$(CFLAGS_$(cdbs_curpkg))","$(CFLAGS)") CXXFLAGS=$(if $(CXXFLAGS_$(cdbs_curpkg)),"$(CXXFLAGS_$(cdbs_curpkg))","$(CXXFLAGS)")
+
+install/fastlink::
+ dh_desktop
Property changes on: trunk/packages/fastlink/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/fastlink/trunk/debian/unknown.1
===================================================================
--- trunk/packages/fastlink/trunk/debian/unknown.1 (rev 0)
+++ trunk/packages/fastlink/trunk/debian/unknown.1 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,78 @@
+.TH UNKNOWN 1 "April 15, 2003"
+.SH NAME
+unknown \- identify possible genotypes for unknowns
+.SH SYNOPSIS
+A program to rapidly identify which genotypes are possible for
+individuals typed as unknowns in the input pedigree.
+.PP
+.B unknown
+[
+.B -cl
+]
+.SH DESCRIPTION
+.B unknown
+infers possible genotypes and mating combinations for parents
+with unknown genotypes for
+.IR ilink (1),
+.IR mlink (1)
+and
+.IR linkmap (1).
+.SH OPTIONS
+.TP
+.B \-c
+Use conditional allele frequencies.
+.TP
+.B \-l
+Choose a good set of loop breakers automatically.
+
+.SH "RETURN VALUE"
+.ta \w'255 'u
+0 Successful completion
+.SH ERRORS
+.nf
+.ta \w'255 'u
+10 File not found
+255 Failure
+.SH EXAMPLES
+Normally,
+.BR unknown (1)
+is run immediately prior to its sister programs,
+.IR ilink (1),
+.IR mlink (1)
+and
+.IR linkmap (1),
+like this:
+
+unknown
+.br
+mlink
+.SH FILES
+.BR unknown (1)
+reads the two files \fIpedfile.dat\fR and \fIdatafile.dat\fR as its
+own input and produces various temporary files that are used as input
+to the next program. These temporary files are \fIipedfile.dat\fR,
+\fIupedfile.dat\fR, \fIspeedfile.dat\fR and \fInewspeedfile.dat\fR.
+
+.SH NOTES
+.BR unknown (1)
+is part of the
+.BR FASTLINK
+package, which is a re-implementation of the
+.BR LINKAGE
+suite of computer tools that help investigate genetic linkage as first
+proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott.
+.SH AUTHORS
+Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work
+originally by Jurg Ott, Ph.D, et. al.
+.PP
+This manual page was written by
+Elizabeth Barham <lizzy at soggytrousers.net> for the Debian GNU/Linux
+system (but may be used by others).
+.SH WORD-WIDE-WEB
+http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+.SH "SEE ALSO"
+.\" Always quote multiple words for .SH
+.IR ilink (1),
+.IR linkmap (1),
+.IR lodscore (1),
+.IR mlink (1).
Added: trunk/packages/fastlink/trunk/debian/unknown.desktop
===================================================================
--- trunk/packages/fastlink/trunk/debian/unknown.desktop (rev 0)
+++ trunk/packages/fastlink/trunk/debian/unknown.desktop 2008-02-18 16:21:26 UTC (rev 1437)
@@ -0,0 +1,12 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Exec=unknown
+Name=unknown
+GenericName=Fastlink identify genotypes
+GenericName[en]=Fastlink identify genotypes
+Comment=Identify possible genotypes for unknowns
+Comment[en]=Identify possible genotypes for unknowns
+Type=Application
+Categories=Biology;Science;Education;
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