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remove public-protected dependency by commeting out some code that should be re-included after all the walkers will be in portected (added some todos)

This commit is contained in:
Ami Levy-Moonshine 2013-01-07 17:07:23 -05:00
parent 8bbb9e1cc2
commit 673ed0aaa6
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -33,7 +33,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pairhmm.ExactPairHMM; import org.broadinstitute.sting.utils.pairhmm.ExactPairHMM;
import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM; //import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM;
import org.broadinstitute.sting.utils.pairhmm.OriginalPairHMM; import org.broadinstitute.sting.utils.pairhmm.OriginalPairHMM;
import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.pairhmm.PairHMM;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
@ -102,9 +102,9 @@ public class PairHMMIndelErrorModel {
break; break;
case CACHING: case CACHING:
case LOGLESS_CACHING: //TODO: still not tested so please do not use yet case LOGLESS_CACHING: //TODO: still not tested so please do not use yet
pairHMM = new LoglessCachingPairHMM(); //pairHMM = new LoglessCachingPairHMM(); //TODO - add it back when the figure out how to use the protected LoglessCachingPairHMM class
System.err.println("warning: this option (LOGLESS_CACHING in UG) is still under development"); throw new UserException.BadArgumentValue("pairHMM"," this option (LOGLESS_CACHING in UG) is still under development");
break; //break;
default: default:
throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING (the third option is still under development)."); throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING (the third option is still under development).");
} }