Merging with upstream changes

README.md

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 # ADEPT
 ADEPT is a GPU accelerated sequence alignment library for short DNA reads and protein sequences. It provides API calls for asychronously performing sequence alignments on GPUs while keeping track of progress on GPUs so that work can be performed on CPUs. Different capabilities of ADEPT API are explored using examples in the `examples` folder.
 
 ## Dependencies
-ADEPT can built using CUDA 9.0 or later and a version of GCC compatible with the CUDA version that is used. 
+ADEPT can be built using CUDA 9.0 or later and a version of GCC compatible with the CUDA version that is used. 
 
-## Examples
-To build the examples cd into the directory containing the <example>.cpp file and use below instructions to build and run:
+## Building
+To build ADEPT library along with the C++ and Python examples, first move into the top level directory of the repo and follow the below steps:
 
-To build:
+### To build:
 ```bash
 mkdir build
 cd build
-cmake ../
+export PYTHONPATH=$PWD:$PYTHONPATH
+cmake -DADEPT_USE_PYTHON=ON ../
 make
 ```
-To run:
+### To run
+To run the installed examples (examples are also used as test):
+```bash
+make test
+```
+If you do not need python module of ADEPT, simply use:
+
 ```bash
-./<example> ../../../test-data/dna-reference.fasta ../../../test-data/dna-query.fasta ./results
+mkdir build
+cd build
+cmake ../
+make
 ```
+and follow the above steps to run the tests.
+
+## Usage
+ADEPT provides Smith Waterman sequence alignment support for Protein and DNA sequences. The library provides options of using multiple GPUs and asynchronous support for performing CPU work while GPUs are busy with ADEPT alignments. To understand different use cases please refer to the samples contained in Examples folder.
 
 ### Contact
 If you need help modifying the library to match your specific use-case or for other issues and bug reports please open an issue or reach out at [email protected]
@@ -33,4 +46,9 @@ If you need help modifying the library to match your specific use-case or for ot
 2. [Muhammad Haseeb](https://sites.google.com/fiu.edu/muhammadhaseeb) [![Twitter](https://flat.badgen.net/twitter/follow/iHaseebM?icon=twitter)](https://twitter.com/iHaseebM)      
 
 ### License
-Please read the license [here](./LICENSE).
+
+ADEPT: a domain independent sequence alignment strategy for GPU architectures Copyright (c) 2019, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+
+If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].
+
+NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.