e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09
max
  Thu Jun 3 08:25:17 2021 -0700
changes after code review, refs #27648

diff --git LICENSE LICENSE
index f92183c..89cc06e 100644
--- LICENSE
+++ LICENSE
@@ -1,52 +1,59 @@
 The default license of this repository is the MIT License, but LICENSE files in
 subdirectories override the text of this LICENSE file.
 
-Therefore the code in this repository falls into three different license types:
+Therefore the code in this repository is covered by five different licenses:
 
-1 the default MIT license (attached below) for code in src/ and most subdirectories
+FREE Licenses:
+
+1. the default MIT license (attached below) for code in src/ and most subdirectories
   - this directory includes all code to build and use tools and libraries to
-    read and write the Genome Browser file formats, like bigBed and bigWig, and
+    read and write the Genome Browser file formats, such as bigBed and bigWig, and
     the command line tools for these, bedToBigBed, wigToBigWig and the tagStorm
     tools and the parasol job scheduler.
   - also, third-party code from open-source projects bundled for convenience,
     in src/htslib (MIT), and ./src/optimalLeaf (public domain, with attribution).
   - the directories src/hg/autoSql and src/hg/autoXml have MIT LICENSE files, so they are also 
     under the MIT License
-2 A non-commercial license from UC for the genome browser website code in
-  src/hg/ and subdirectories (see src/hg/LICENSE), see https://genome-store.ucsc.edu/
-3 A non-commercial license from Kent Informatics for the BLAT code in src/blat/ and
-  src/jkOwnLib/, see http://www.kentinformatics.com/
+2. A modified BSD license for src/htslib/cram/, see src/htslib/LICENSE. 
+   Copyright (C) 2012-2014 Genome Research Ltd.
+3. Public domain "with attribution" license, see src/optimalLeaf/LICENSE
+
+NON-COMMERCIAL licenses:
+
+4. A non-commercial license from UC for the genome browser website code in src/hg/ 
+   and subdirectories (see src/hg/LICENSE), see https://genome.ucsc.edu/license/
+5. A non-commercial license from Kent Informatics for the BLAT and isPCR code in src/blat/ and
+   src/jkOwnLib/, for more information see https://genome.ucsc.edu/license/ and http://www.kentinformatics.com/
 
-See https://genome.ucsc.edu/license/ for more details and on how to obtain a license.
+See https://genome.ucsc.edu/license/ for more details and on how to obtain a license
+for commercial use for the cases (4) and (5). Commercial users should contact
+kent@soe.ucsc.edu for access to other modules including jkOwnLib and blat.
+
+Commercial users interested in the UCSC Genome Browser in particular please see
+    http://genome.ucsc.edu/license/.
 
+The code in src/htslib is distributed with two licenses as noted in the LICENSE
+file in that directory.
 ---- 
 
 MIT License
 
 Copyright (C) 2001 UC Regents
 
 Permission is hereby granted, free of charge, to any person or non-commercial
 entity obtaining a copy of this software and associated documentation files (the
 "Software"), to deal in the Software without restriction, including without
 limitation the rights to use, copy, modify, merge, publish, distribute,
 sublicense, and/or sell copies of the Software, and to permit persons to whom
 the Software is furnished to do so, subject to the following conditions:
 
 The above copyright notice and this permission notice shall be included in all
 copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-Commercial users should contact kent@soe.ucsc.edu for access to other modules
-including jkOwnLib and blat.
-
-Commercial users interested in the UCSC Genome Browser in particular please see
-    http://genome.ucsc.edu/license/.
-
-The code in /src/htslib is distributed with two licenses as noted in the LICENSE
-file in that directory.