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better error message

This commit is contained in:
Ami Levy-Moonshine 2013-01-03 13:41:03 -05:00
parent 53f8be96d2
commit 2018285a39
1 changed files with 2 additions and 1 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -103,9 +103,10 @@ public class PairHMMIndelErrorModel {
case CACHING: case CACHING:
case LOGLESS_CACHING: case LOGLESS_CACHING:
pairHMM = new LoglessCachingPairHMM(); pairHMM = new LoglessCachingPairHMM();
System.err.println("warning: 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 and EXACT."); 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).");
} }
// fill gap penalty table, affine naive model: // fill gap penalty table, affine naive model: