@Config.LoadPolicy(value=MERGE)
@Config.Sources(value={"file:${GATKConfig.pathToGatkConfig}","classpath:${GATKConfig.classPathToGatkConfig}","file:GATKConfig.properties","classpath:org/broadinstitute/hellbender/utils/config/GATKConfig.properties"})
public interface GATKConfig
extends org.aeonbits.owner.Mutable, org.aeonbits.owner.Accessible
Sources will be loaded.
The Config.LoadPolicy is set to Config.LoadType.MERGE, which specifies that if a configuration option is not found
in the first source, the option will be sought in all following sources until a definition is found.
If the option is not specified in any file, the coded default value will be used (as defined by @DefaultValue).
The load order is always resolved "top-down" by declaration order in the @Sources annotation.
In this case, the load order is:
1) "file:${" + GATKConfig.CONFIG_FILE_VARIABLE_FILE_NAME + "}",
2) "classpath:${" + GATKConfig.CONFIG_FILE_VARIABLE_CLASS_PATH + "}",
3) "file:GATKConfig.properties",
4) "classpath:org/broadinstitute/hellbender/utils/config/GATKConfig.properties"
5) hard-coded values specified by @DefaultValueorg.aeonbits.owner.Config.ConverterClass, org.aeonbits.owner.Config.DefaultValue, org.aeonbits.owner.Config.DisableableFeature, org.aeonbits.owner.Config.DisableFeature, org.aeonbits.owner.Config.HotReload, org.aeonbits.owner.Config.HotReloadType, org.aeonbits.owner.Config.Key, org.aeonbits.owner.Config.LoadPolicy, org.aeonbits.owner.Config.LoadType, org.aeonbits.owner.Config.PreprocessorClasses, org.aeonbits.owner.Config.Separator, org.aeonbits.owner.Config.Sources, org.aeonbits.owner.Config.TokenizerClass| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
CONFIG_FILE_VARIABLE_CLASS_PATH
Name of the configuration file variable to be used in the
Config.Sources annotation for GATKConfig
as a place to find the configuration file corresponding to this interface. |
static java.lang.String |
CONFIG_FILE_VARIABLE_FILE_NAME
Name of the configuration file variable to be used in the
Config.Sources annotation for GATKConfig
as a place to find the configuration file corresponding to this interface. |
static java.lang.String |
DEFAULT_ANNOTATION_PACKAGES |
| Modifier and Type | Method and Description |
|---|---|
java.util.List<java.lang.String> |
annotation_packages() |
int |
cloudIndexPrefetchBuffer() |
int |
cloudPrefetchBuffer() |
java.util.List<java.lang.String> |
codec_packages() |
boolean |
createOutputBamIndex() |
boolean |
gatk_stacktrace_on_user_exception() |
int |
gcsMaxRetries() |
java.lang.String |
gcsProjectForRequesterPays() |
java.util.List<java.lang.String> |
read_filter_packages() |
int |
samjdk_compression_level() |
java.lang.Boolean |
samjdk_use_async_io_read_samtools() |
boolean |
samjdk_use_async_io_write_samtools() |
boolean |
samjdk_use_async_io_write_tribble() |
java.lang.String |
spark_driver_extraJavaOptions() |
int |
spark_driver_maxResultSize() |
boolean |
spark_driver_userClassPathFirst() |
java.lang.String |
spark_executor_extraJavaOptions() |
int |
spark_executor_memoryOverhead() |
java.lang.String |
spark_io_compression_codec() |
java.lang.String |
spark_kryoserializer_buffer_max() |
static final java.lang.String CONFIG_FILE_VARIABLE_FILE_NAME
Config.Sources annotation for GATKConfig
as a place to find the configuration file corresponding to this interface.static final java.lang.String CONFIG_FILE_VARIABLE_CLASS_PATH
Config.Sources annotation for GATKConfig
as a place to find the configuration file corresponding to this interface.static final java.lang.String DEFAULT_ANNOTATION_PACKAGES
@SystemProperty @Config.Key(value="gatk_stacktrace_on_user_exception") @Config.DefaultValue(value="false") boolean gatk_stacktrace_on_user_exception()
@SystemProperty @Config.Key(value="samjdk.use_async_io_read_samtools") @Config.ConverterClass(value=CustomBooleanConverter.class) @Config.DefaultValue(value="false") java.lang.Boolean samjdk_use_async_io_read_samtools()
@SystemProperty @Config.Key(value="samjdk.use_async_io_write_samtools") @Config.DefaultValue(value="true") boolean samjdk_use_async_io_write_samtools()
@SystemProperty @Config.Key(value="samjdk.use_async_io_write_tribble") @Config.DefaultValue(value="false") boolean samjdk_use_async_io_write_tribble()
@SystemProperty @Config.Key(value="samjdk.compression_level") @Config.DefaultValue(value="2") int samjdk_compression_level()
@SystemProperty @Config.Key(value="spark.kryoserializer.buffer.max") @Config.DefaultValue(value="512m") java.lang.String spark_kryoserializer_buffer_max()
@SystemProperty @Config.Key(value="spark.driver.maxResultSize") @Config.DefaultValue(value="0") int spark_driver_maxResultSize()
@SystemProperty @Config.Key(value="spark.driver.userClassPathFirst") @Config.DefaultValue(value="true") boolean spark_driver_userClassPathFirst()
@SystemProperty @Config.Key(value="spark.io.compression.codec") @Config.DefaultValue(value="lzf") java.lang.String spark_io_compression_codec()
@SystemProperty @Config.Key(value="spark.executor.memoryOverhead") @Config.DefaultValue(value="600") int spark_executor_memoryOverhead()
@SystemProperty @Config.Key(value="spark.driver.extraJavaOptions") @Config.DefaultValue(value="") java.lang.String spark_driver_extraJavaOptions()
@SystemProperty @Config.Key(value="spark.executor.extraJavaOptions") @Config.DefaultValue(value="") java.lang.String spark_executor_extraJavaOptions()
@Config.DefaultValue(value="htsjdk.variant,htsjdk.tribble,org.broadinstitute.hellbender.utils.codecs") java.util.List<java.lang.String> codec_packages()
@Config.DefaultValue(value="org.broadinstitute.hellbender.engine.filters") java.util.List<java.lang.String> read_filter_packages()
@Config.DefaultValue(value="org.broadinstitute.hellbender.tools.walkers.annotator") java.util.List<java.lang.String> annotation_packages()
@Config.DefaultValue(value="40") int cloudPrefetchBuffer()
@Config.DefaultValue(value="-1") int cloudIndexPrefetchBuffer()
@Config.DefaultValue(value="20") int gcsMaxRetries()
@Config.DefaultValue(value="") java.lang.String gcsProjectForRequesterPays()
@Config.DefaultValue(value="true") boolean createOutputBamIndex()