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setting default compression level to 2 (broadinstitute#4547)
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changing the default compression level 1 -> 2
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lbergelson authored and cwhelan committed May 25, 2018
1 parent 01cf02c commit 71ac858
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Showing 4 changed files with 6 additions and 6 deletions.
4 changes: 2 additions & 2 deletions build.gradle
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Expand Up @@ -29,7 +29,7 @@ import javax.tools.ToolProvider
mainClassName = "org.broadinstitute.hellbender.Main"

//Note: the test suite must use the same defaults. If you change system properties in this list you must also update the one in the test task
applicationDefaultJvmArgs = ["-Dsamjdk.use_async_io_read_samtools=false","-Dsamjdk.use_async_io_write_samtools=true", "-Dsamjdk.use_async_io_write_tribble=false", "-Dsamjdk.compression_level=1"]
applicationDefaultJvmArgs = ["-Dsamjdk.use_async_io_read_samtools=false","-Dsamjdk.use_async_io_write_samtools=true", "-Dsamjdk.use_async_io_write_tribble=false", "-Dsamjdk.compression_level=2"]

//Delete the windows script - we never test on Windows so let's not pretend it works
startScripts {
Expand Down Expand Up @@ -340,7 +340,7 @@ test {
systemProperty "samjdk.use_async_io_read_samtools", "false"
systemProperty "samjdk.use_async_io_write_samtools", "true"
systemProperty "samjdk.use_async_io_write_tribble", "false"
systemProperty "samjdk.compression_level", "1"
systemProperty "samjdk.compression_level", "2"
systemProperty "gatk.spark.debug", System.getProperty("gatk.spark.debug")

environment "SPARK_LOCAL_IP","127.0.0.1"
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4 changes: 2 additions & 2 deletions gatk
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Expand Up @@ -37,12 +37,12 @@ EXTRA_JAVA_OPTIONS_SPARK= "-DGATK_STACKTRACE_ON_USER_EXCEPTION=true " \
"-Dsamjdk.use_async_io_read_samtools=false " \
"-Dsamjdk.use_async_io_write_samtools=false " \
"-Dsamjdk.use_async_io_write_tribble=false " \
"-Dsamjdk.compression_level=1 "
"-Dsamjdk.compression_level=2 "

PACKAGED_LOCAL_JAR_OPTIONS= ["-Dsamjdk.use_async_io_read_samtools=false",
"-Dsamjdk.use_async_io_write_samtools=true",
"-Dsamjdk.use_async_io_write_tribble=false",
"-Dsamjdk.compression_level=1"]
"-Dsamjdk.compression_level=2"]

DEFAULT_SPARK_ARGS_PREFIX = '--conf'
DEFAULT_SPARK_ARGS = {
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ public interface GATKConfig extends Mutable, Accessible {

@SystemProperty
@Key("samjdk.compression_level")
@DefaultValue("1")
@DefaultValue("2")
int samjdk_compression_level();

// ----------------------------------------------------------
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Expand Up @@ -41,7 +41,7 @@ gatk_stacktrace_on_user_exception = false
samjdk.use_async_io_read_samtools = false
samjdk.use_async_io_write_samtools = true
samjdk.use_async_io_write_tribble = false
samjdk.compression_level = 1
samjdk.compression_level = 2

# ----------------------------------------------------------
# Spark Options:
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