This is a patch to fix a problem in pileup_v0.5
where large insert sizes are cut off.
HP090512

Place the file ssaha_clean.c in the pilup path at 
pileup_v0.5/ssaha_pileup/ssaha_pileup/ssaha_clean.c

then change to the top directory and run the install script ./install.csh


For example, if the pileup directory is

/nfs/team81/jit/bin/pileup_v0.5

then do the following:

> cp pileup_v0.5_patch1/ssaha_clean.c /nfs/team81/jit/bin/pileup_v0.5/ssaha_pileup/ssaha_pileup/ssaha_clean.c
> cd /nfs/team81/jit/bin/pileup_v0.5/
> ./install.csh

Finally place the updates wrapper script in the correct directory:
> cp pileup_v0.5_patch1/pileup.NoPile.csh  /nfs/team81/jit/bin/pileup_v0.5/.
