diff --git a/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java b/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java index 6f9f2749b..03f7be477 100644 --- a/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java +++ b/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java @@ -38,8 +38,6 @@ public class FourBaseRecaller extends CommandLineProgram { public Boolean RAW = false; @Argument(fullName="old", shortName="1", doc="Old Bustard 1.1 mode?", required=false) public Boolean OLD = false; - @Argument(fullName="context", shortName="X", doc="Correct for context?", required=false) - public Boolean CONTEXT = false; public static void main(String[] argv) { Instance = new FourBaseRecaller(); @@ -70,7 +68,7 @@ public class FourBaseRecaller extends CommandLineProgram { fread = ffp.next(); int cycle_offset = (END <= 1) ? 0 : bread.getIntensities().length/2; - BasecallingReadModel model = new BasecallingReadModel(bread.getFirstReadSequence().length(), CONTEXT); + BasecallingReadModel model = new BasecallingReadModel(bread.getFirstReadSequence().length()); int queryid; // learn mean parameters