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update license

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1 parent 22319db commit 9e79ade97ba05ea4ad959f3e45c34ef780b6fba9 @mdcao committed Oct 24, 2016
Showing with 200 additions and 158 deletions.
  1. +1 −1 LICENSE.md
  2. +4 −0 src/main/java/japsa/bio/alignment/ProfileDP.java
  3. +195 −157 src/main/java/japsa/tools/bio/hts/VNTRLongReadsCmd.java
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@@ -1,4 +1,4 @@
- Copyright (c) Minh Duc Cao, Monash Uni & UQ, All rights reserved.
+ Copyright (c) the author(s), All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
@@ -119,6 +119,10 @@ public void setMatchProbability(double matP){
matchCost = - JapsaMath.log2(matchProb);
misMatchCost = -JapsaMath.log2(misMatchProb)- JapsaMath.log2(1.0/3.0);;
}
+
+ public int getProfileLength(){
+ return profileSeq.length();
+ }
/**************************************************/
public EmissionState align(Sequence seq){
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