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Commented out some debugging lines 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@415 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-14 20:15:41 +00:00
parent 49d76014d1
commit 222c4e5865
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -314,7 +314,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
posterior_null_hyp = P_D_q(bases, quals, 0.0, refnum, altnum) + P_q_G(bases, N, 0.0, 0, 0) + P_G(N, 0);
bestMixtures[0] = new MixtureLikelihood(posterior_null_hyp, 0.0, 0.0);
System.out.format("DBG %s %.2f %.2f %5.2f %5.2f %5.2f %5.2f %d %d %s\n", location, 0.0, 0.0, P_D_q(bases, quals, 0.0, refnum, altnum), P_q_G(bases, N, 0.0, 0, 0), P_G(N, 0), posterior_null_hyp, (int)(q*bases.length), (int)((1.0-q)*bases.length), new String(bases));
//System.out.format("DBG %s %.2f %.2f %5.2f %5.2f %5.2f %5.2f %d %d %s\n", location, 0.0, 0.0, P_D_q(bases, quals, 0.0, refnum, altnum), P_q_G(bases, N, 0.0, 0, 0), P_G(N, 0), posterior_null_hyp, (int)(q*bases.length), (int)((1.0-q)*bases.length), new String(bases));
// qstar - true allele balances
//for (qstar = epsilon + ((1.0 - 2*epsilon)/N), qstar_N = 1; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N, qstar_N++)
@ -328,7 +328,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
bestMixtures[qstar_N] = new MixtureLikelihood(posterior, qstar, q);
System.out.format("DBG %s %.2f %.2f %5.2f %5.2f %5.2f %5.2f %d %d %s\n", location, q, qstar, pDq, pqG, pG, posterior, (int)(q*bases.length), (int)((1.0-q)*bases.length), new String(bases));
//System.out.format("DBG %s %.2f %.2f %5.2f %5.2f %5.2f %5.2f %d %d %s\n", location, q, qstar, pDq, pqG, pG, posterior, (int)(q*bases.length), (int)((1.0-q)*bases.length), new String(bases));
}
}