Make FIJ and Find Read Pairs sub-commands open in read-only mode as
they have no strong need to be read-write.

However possibly we should add a -rw command line option to force
read-write still as some actions of these tools could generate data
which is best cached (eg consensus, read-pair locations).


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3511 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Make distsrc now also generates a tarball


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3512 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added $STADENROOT/lib to LD_LIBRARY_PATH too so we can add any
third-party libraries (ie not part of the staden package) in there to
override any system versions or to ensure libraries exist. This is
particularly relevant to the MacOS X build.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3513 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Minor optimisation


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3514 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Nearing the next release so updated version and changelog. More to go
still, specifically Windows and a few bugs uncovered.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3515 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Cosmetic code tidyup. Lines longer than 80 characters offend me!


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3516 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Stopped parse_acd_tag from returning pointers beyond the end of the string.

If parse_acd_tag tag was handed a string that did not end in \n, it would
return a pointer to 1 past the NUL byte on the end.  This would cause it
to attempt to read uninitialized memory when called next time.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3517 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added #include <io.h> to the MINGW part of os.h so the chdir() macro
is applied after the system definition. This avoids errors if we
include os.h before io.h and then get an illegal system head file.

Unfortunately adding this breaks Gap4's IO.h (and .c) as on windows
IO.h and io.h are the same file. So renamed these to IO1.c and IO1.h,
given we have IO2.c and IO3.c already, updated the myriad of places
they were included from and reran make depend too.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3518 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Renamed tkpWinRopModes to a static sp_tkpWinRopModes to avoid clashes
with the same named variable in tk8.6 distribution.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3519 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Switched to using ckalloc and ckfree for image->buf as this is copied
into the XImage and sometimes freed by Tcl. (On windows if tcl frees it
we must allocate it using ckalloc.)


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3520 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Renamed #ifdef _IO_H_ guard. Forgot this in io to io1 rename.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3521 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed mouse wheel bindings for Windows in template display and contig
editor.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3522 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1