The old sequence library compiles and the examples work on Cygwin.
Here is my Cygwin Setup
$ gcc -v
Reading specs from /usr/lib/gcc-lib/i686-pc-cygwin/2.95.3-5/specs
gcc version 2.95.3-5 (cygwin special)
$ uname -a
CYGWIN_NT-5.0 C1651700-A 1.3.3(0.46/3/2) 2001-09-12 23:54 i686 unknown
I made a quick change in the code and got the seqio to compile. The examples seem to work provided test data that I borrowed from bioperl.
But all and all its good news. The other files in the old library do not compile as of yet but they aren't high priority as they aren't the library but rather just helpful functions.
libSeqIO has offically started. I checked in the initial release, which happens to be James Knight's C library seqio. To start I'll get the C library to compile and start designing the interfaces for the real libSeqIO.