From 673ed0aaa67d6b2d49e654ecce317e0b8175e48e Mon Sep 17 00:00:00 2001 From: Ami Levy-Moonshine Date: Mon, 7 Jan 2013 17:07:23 -0500 Subject: [PATCH] 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) --- .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 221093759..5f0407b13 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.exceptions.UserException; 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.PairHMM; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -102,9 +102,9 @@ public class PairHMMIndelErrorModel { break; case CACHING: case LOGLESS_CACHING: //TODO: still not tested so please do not use yet - pairHMM = new LoglessCachingPairHMM(); - System.err.println("warning: this option (LOGLESS_CACHING in UG) is still under development"); - break; + //pairHMM = new LoglessCachingPairHMM(); //TODO - add it back when the figure out how to use the protected LoglessCachingPairHMM class + throw new UserException.BadArgumentValue("pairHMM"," this option (LOGLESS_CACHING in UG) is still under development"); + //break; 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)."); }