Licence clarified. Updated fusion pair list.

LICENSE

@@ -0,0 +1,21 @@
+T License (MIT)
+
+Copyright (c) 2014 AstraZeneca - NGS Team
+
+Permission is hereby granted, free of charge, to any person 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.

README.md

@@ -35,12 +35,18 @@ vcf FILE - vcf file annotated with snpEff v4.1g+
 **Optional arguments**
 
 ```
---output/-o   FILE - Output file name. Default: <invcf>.simpleann.vcf
+--output/-o   FILE - Output file name. Use dash (-) for stdout. Default: <invcf>.simpleann.vcf.
 --exonNums/-e FILE - List of custom exon numbers (see Alternate Exon Numbers)
 --gene_list/-g FILE - List of genes to prioritise on
 --known_fusion_pairs/-k FILE - Comma delimited file with a gene pair on each row representing known fusion pairs
 ```
 
+## Licence
+
+This program is distributed under the MIT licence save for the exception below.
+
+The file ```fusion_pairs.txt``` provided here is an extract of the file at https://github.com/ndaniel/fusioncatcher/blob/master/bin/generate_known.py and is redistributed here under the GNU GPLv3. 
+
 ## Alternate Exon Numbers
 
 Occasionally the exon numbering scheme provided by snpEff is incorrect. snpEff
@@ -122,7 +128,7 @@ specifications are followed and each SV is described with standard SV INFO field
 
 ## Example Output
 
-There are two different outputs that ```simple_sv_annotation.py``` can produce:
+Primary output for ```simple_sv_annotation.py```:
 
 #### 1. Add SIMPLE_ANN field