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Move warnings to debug logging status because they will definitely scare users

This commit is contained in:
Eric Banks 2014-03-05 15:05:21 -05:00
parent 5b55380bdf
commit d3de6413c9
2 changed files with 4 additions and 4 deletions
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2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
View File

@ -97,7 +97,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
} }
catch(UnsatisfiedLinkError ule) 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(); return new LoglessPairHMM();
} }
case DEBUG_VECTOR_LOGLESS_CACHING: case DEBUG_VECTOR_LOGLESS_CACHING:

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
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@ -133,9 +133,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
//Could not load from Java's library path - try unpacking from jar //Could not load from Java's library path - try unpacking from jar
try 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"); 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) 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. * 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. * 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 IOException If temporary file creation or read/write operation fails
* @throws IllegalArgumentException If source file (param path) does not exist * @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)}). * @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)}).