9c0f463152095051a207201ce8d28eec87a1aaaa
hiram
  Tue Dec 6 13:39:52 2016 -0800
per Jim request, adding copyright information to a couple README files refs #13978

diff --git src/hg/liftOver/README.txt src/hg/liftOver/README.txt
index 15a9f9c..c09cb66 100644
--- src/hg/liftOver/README.txt
+++ src/hg/liftOver/README.txt
@@ -1,30 +1,45 @@
+LICENSE
+
+The Genome Browser binaries and source code are freely available for
+academic, nonprofit, and personal use.  A license is required for
+commercial download and installation of most Genome Browser binaries
+and source code, with the exception of specific items in some directories
+that are freely available for all uses.  Please note the current
+license infomation with the list of specific directory permissions:
+
+   http://genome.ucsc.edu/license/
+
+=============================================================================
+
+   kent/src/hg/liftOver/
+
 LiftOver has additional optional arguments for use with cross-species lifts:
 
    -multiple               Allow multiple output regions
    -minSizeT, -minSizeQ    Minimum chain size in target/query,
                              when mapping to multiple output regions
                                      (default 0, 0)
 
 Depending on the size of the region being mapped, the species distance
 and the quality of the assembly, the user may need to adjust the
 minimum chain sizes.  For ENCODE regions (.5 to 1.8 MB), I used
 
     -minSizeT=4000
 and
     -minSizeQ=20000
         for mammals except chimp, which, due to the fragmented
         assembly, I reduced minSizeQ to 10000
     -minSizeQ=1000
         for non-mammals (bird & fish)
 
 Also, for cross-species, they'll want to set the -minMatch very low
 (e.g. .01), instead of the default .95, which is a reasonable default
 for within species.
 
 Hmmm, sounds like this should be a README in our liftOver downloads dirs.
 
 Finally, there's an additional tool, liftOverMerge, which is useful
 when lifting large regions.  I used it for ENCODE, but don't think
 it likely that users will need it.
 
         Kate