On a UNIX system, when an application reads from a file it gets exactly what's in the file on disk and the converse is true for writing. The situation is different in the DOS/Windows world where a file can be opened in one of two modes, binary or text. In the binary mode the system behaves exactly as in UNIX. However in text mode there are major differences: On writing in text mode, a NL (\n, ^J) is transformed into the sequence CR (\r, ^M) NL. On reading in text mode, a CR followed by an NL is deleted and a ^Z character signals the end of file. This can wreak havoc with the seek/fseek calls since the number of bytes actually in the file may differ from that seen by the application. The mode can be specified explicitly as explained in the Programming section below. In an ideal DOS/Windows world, all programs using lines as records (such as bash, make, sed ...) would open files (and change the mode of their standard input and output) as text. All other programs (such as cat, cmp, tr ...) would use binary mode. In practice with Cygwin, programs that deal explicitly with object files specify binary mode (this is the case of od, which is helpful to diagnose CR problems). Most other programs (such as cat, cmp, tr) use the default mode. The Cygwin system gives us some flexibility in deciding how files are to be opened when the mode is not specified explicitly. The rules are evolving, this section gives the design goals. If the file appears to reside on a file system that is mounted (i.e. if its pathname starts with a directory displayed by mount), then the default is specified by the mount flag. If the file is a symbolic link, the mode of the target file system applies. If the file appears to reside on a file system that is not mounted (as can happen when the path contains a drive letter), the default is text. Pipes and non-file devices are opened in binary mode, except if the CYGWIN environment variable contains nobinmode. In b20.1 of 12/98, a file will be opened in binary mode if any of the following conditions hold: binary mode is specified in the open call CYGWIN contains binmode the file resides in a binary mounted partition the file is not a disk file When a Cygwin program is launched by a shell, its standard input, output and error are in binary mode if the CYGWIN variable contains tty, else in text mode, except if they are piped or redirected. When redirecting, the Cygwin shells uses rules (a-c). For these shells the relevant value of CYGWIN is that at the time the shell was launched and not that at the time the program is executed. Non-Cygwin shells always pipe and redirect with binary mode. With non-Cygwin shells the commands cat filename | program and program < filename are not equivalent when filename is on a text-mounted partition. To illustrate the various rules, we provide scripts to delete CRs from files by using the tr program, which can only write to standard output. The script "$1".nocr ]]> will not work on a text mounted systems because the \r will be reintroduced on writing. However scripts such as "$1".nocr ]]> and the .bat file %1.nocr ]]> work fine. In the first case (assuming the pipes are binary) we rely on gunzip to set its output to binary mode, possibly overriding the mode used by the shell. In the second case we rely on the DOS shell to redirect in binary mode. UNIX programs that have been written for maximum portability will know the difference between text and binary files and act appropriately under Cygwin. For those programs, the text mode default is a good choice. Programs included in official Cygwin distributions should work well in the default mode. Text mode makes it much easier to mix files between Cygwin and Windows programs, since Windows programs will usually use the CRLF format. Unfortunately you may still have some problems with text mode. First, some of the utilities included with Cygwin do not yet specify binary mode when they should, e.g. cat will not work with binary files (input will stop at ^Z, CRs will be introduced in the output). Second, you will introduce CRs in text files you write, which can cause problems when moving them back to a UNIX system. If you are mounting a remote file system from a UNIX machine, or moving files back and forth to a UNIX machine, you may want to access the files in binary mode. The text files found there will normally be in UNIX NL format, and you would want any files put there by Cygwin programs to be stored in a format understood by UNIX. Be sure to remove CRs from all Makefiles and shell scripts and make sure that you only edit the files with DOS/Windows editors that can cope with and preserve NL terminated lines. Note that you can decide this on a disk by disk basis (for example, mounting local disks in text mode and network disks in binary mode). You can also partition a disk, for example by mounting c: in text mode, and c:\home in binary mode. In the open() function call, binary mode can be specified with the flag O_BINARY and text mode with O_TEXT. These symbols are defined in fcntl.h. In the fopen() function call, binary mode can be specified by adding a b to the mode string. There is no direct way to specify text mode. The mode of a file can be changed by the call setmode(fd,mode) where fd is a file descriptor (an integer) and mode is O_BINARY or O_TEXT. The function returns O_BINARY or O_TEXT depending on the mode before the call, and EOF on error.