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Updated to reflect change to BasecallingReadModel constructor. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-20 15:43:26 +00:00
parent 505f588768
commit e48078b476
1 changed files with 1 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
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@ -38,8 +38,6 @@ public class FourBaseRecaller extends CommandLineProgram {
public Boolean RAW = false; public Boolean RAW = false;
@Argument(fullName="old", shortName="1", doc="Old Bustard 1.1 mode?", required=false) @Argument(fullName="old", shortName="1", doc="Old Bustard 1.1 mode?", required=false)
public Boolean OLD = 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) { public static void main(String[] argv) {
Instance = new FourBaseRecaller(); Instance = new FourBaseRecaller();
@ -70,7 +68,7 @@ public class FourBaseRecaller extends CommandLineProgram {
fread = ffp.next(); fread = ffp.next();
int cycle_offset = (END <= 1) ? 0 : bread.getIntensities().length/2; 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; int queryid;
// learn mean parameters // learn mean parameters