Merge branch 'master' of https://github.com/mckennalab/FlashFry

Author: aaronmck

README.md

@@ -31,7 +31,7 @@ The easiest way to get started it to try out the quick-start procedure to make s
 First, make sure you're running Java version 8 (type ```java -version``` on the command line to see the version). From the UNIX or Mac command line, download the latest release version of the FlashFry jar file:
 
 ```shell
-wget https://github.com/mckennalab/FlashFry/releases/download/1.11/FlashFry-assembly-1.11.jar
+wget https://github.com/mckennalab/FlashFry/releases/download/1.12/FlashFry-assembly-1.12.jar
 ```
 Download and then un-gzip the sample data for human chromosome 22:
 
@@ -44,7 +44,7 @@ Then run the database creation step (this should take a few minutes, it takes ~7
 
 ```shell
 mkdir tmp
-java -Xmx4g -jar FlashFry-assembly-1.11.jar \
+java -Xmx4g -jar FlashFry-assembly-1.12.jar \
  index \
  --tmpLocation ./tmp \
  --database chr22_cas9ngg_database \
@@ -55,7 +55,7 @@ java -Xmx4g -jar FlashFry-assembly-1.11.jar \
 Now we discover candidate targets and their potential off-target in the test data (takes a few seconds). Here we're using the EMX1 target with some random sequence flanking the target site:
 
 ```shell
-java -Xmx4g -jar FlashFry-assembly-1.11.jar \
+java -Xmx4g -jar FlashFry-assembly-1.12.jar \
  discover \
  --database chr22_cas9ngg_database \
  --fasta EMX1_GAGTCCGAGCAGAAGAAGAAGGG.fasta \
@@ -65,7 +65,7 @@ java -Xmx4g -jar FlashFry-assembly-1.11.jar \
 Finally we score the discovered sites (a few seconds):
 
 ```shell
-java -Xmx4g -jar FlashFry-assembly-1.11.jar \
+java -Xmx4g -jar FlashFry-assembly-1.12.jar \
  score \
  --input EMX1.output \
  --output EMX1.output.scored \