FASTLINK for DOS

Fundamental: We distribute 5 executables

      ilink.exe
      linkmap.exe
      lodscore.exe
      mlink.exe
      unknown.exe

These can be plugged in directly instead of the similarly-named LINKAGE for DOS executables. An easy way to do this is to have separate directories for LINKAGE and FASTLINK. If you put the FASTLINK directory ahead of the LINKAGE directory in your default path, DOS will find the FASTLINK executables when appropriate, and will continue to use the LINKAGE executables for the auxiliary programs: lcp, lsp, lrp, makeped, preplink.

Some fundamental similarities and differences between UNIX versions and DOS versions should be noted:

Similarities:

1. DOS FASTLINK is essentially the same as FASTLINK 3.0P, provided that the computer does not crash during the run.
2. Most of the documenatation still applies except the instructions for installation (we distribute executables for DOS, so no compilation is required) and portability (basically irrelevant to DOS).
3. We are distributing versions of LODSCORE, ILINK, LINKMAP, MLINK, UNKNOWN. Other auxiliary programs can be obtained from the FTP site at Columbia.

Differences:

1. We are distributing executable versions for DOS FASTLINK, rather than source as for UNIX FASTLINK. Details about how to get the executables are given below.
2. The source code for FASTLINK for DOS is the same as the non-DOS source code. However, if you wish to get source code and compile it, you should use the djgpp C compiler; this is a port of the gcc compiler to DOS. Instructions for retrieving and installing the compiler are in README.djgpp . djgpp is freely available over the Internet by ftp.
3. DOS FASTLINK does not support crash recovery.
4. We are distributing only the "slow" versions of FASTLINK for now. These are still measurably faster than LINKAGE.

Cautions:

1. FASTLINK is derived from LINKAGE 5.1 for UNIX and not from LINKAGE for DOS. We have tested FASTLINK on DOS, but we have not investigated to what extent LINKAGE for UNIX and LINKAGE for DOS are incompatible.
2. If FASTLINK and LINKAGE give different answers, you should not assume that FASTLINK is wrong. LINKAGE may be wrong. I have fixed 2 significant bugs in LINKAGE LODSCORE/ILINK and 1 significant bug in LINKAGE LINKMAP/MLINK. These bug fixes are described in README.updates . There is also an inconsistency in scaling in LINKAGE LINKMAP, which is fixed in FASTLINK LINKMAP (see README.scaling ).
3. You must a have 386 or higher machine. The code was tested on several different 486 machines. I am fairly certain that it won't work on 286 and below machines.
4. You should have a Math co-processor on the machine. Most recent 486 machines will have this.
5. We strongly recommend trying the programs outside of Windows (i.e., in vanilla DOS) first. They probably work from Windows too, but it may be the case that the compiler makes some assumptions about how the video/monitor environment is set up, which are not consistent with the setup of your machine.

Like FASTLINK for UNIX and VMS, FASTLINK for DOS is distributed by FTP from a computer at Rice University. Contact me by e-mail at schaffer@nchgr.nih.gov if you want the executables mailed to you on floppy disks.

Here are the instructions for retrieving the code:

   ftp softlib.cs.rice.edu

   cd pub/fastlink/dos
   binary

[For those who receive FASTLINK for DOS on 3.5" diskettes, the documentation is on one of the diskettes and the sticky labels tell you which it is.]

For those who retrieve the files via ftp. Having retrieved whatever documentation you want, you should retrieve:

   lodscore.exe
   ilink.exe
   linkmap.exe
   mlink.exe
   unknown.exe

You should retrieve all 5 files. You must use the FASTLINK version of UNKNOWN with the FASTLINK main programs. Remember to use binary mode in FTP. Previous versions had a limit on the number of haplotypes; this limit has been eliminated in FASTLINK 3.0P.

Note: The DOS executables are not currently included in fastlink.tar.Z, so you must retrieve them as individual files.