diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index c1a1f68f1..7165e61a5 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -97,7 +97,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation } catch(UnsatisfiedLinkError ule) { - logger.warn("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING"); + logger.debug("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING"); return new LoglessPairHMM(); } case DEBUG_VECTOR_LOGLESS_CACHING: diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java index a32768c20..f27081ae9 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java @@ -133,9 +133,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM { //Could not load from Java's library path - try unpacking from jar try { - logger.info("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar"); + logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar"); loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so"); - logger.info("libVectorLoglessPairHMM unpacked successfully from StingUtils.jar"); + logger.debug("libVectorLoglessPairHMM unpacked successfully from StingUtils.jar"); } catch(IOException ioe) { @@ -269,7 +269,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM { * The file from JAR is copied into system temporary directory and then loaded. The temporary file is deleted after exiting. * Method uses String as filename because the pathname is "abstract", not system-dependent. * - * @param filename The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext + * @param path The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext * @throws IOException If temporary file creation or read/write operation fails * @throws IllegalArgumentException If source file (param path) does not exist * @throws IllegalArgumentException If the path is not absolute or if the filename is shorter than three characters (restriction of {@see File#createTempFile(java.lang.String, java.lang.String)}).