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upgrading to spark 2.2.0 #4314

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merged 2 commits into from
Mar 26, 2018
Merged

upgrading to spark 2.2.0 #4314

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36ea14e
upgrading to spark 2.2.0
lbergelson Jan 31, 2018
7bd7707
updating hadoop version to match the version in dataproc
lbergelson Jan 31, 2018
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7 changes: 4 additions & 3 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,8 @@ repositories {
final htsjdkVersion = System.getProperty('htsjdk.version','2.14.1')
final picardVersion = System.getProperty('picard.version','2.17.2')
final barclayVersion = System.getProperty('barclay.version','2.1.0')
final sparkVersion = System.getProperty('spark.version', '2.0.2')
final sparkVersion = System.getProperty('spark.version', '2.2.0')
final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
final hadoopBamVersion = System.getProperty('hadoopBam.version','7.9.1')
final genomicsdbVersion = System.getProperty('genomicsdb.version','0.9.2-proto-3.0.0-beta-1+uuid-static')
final testNGVersion = '6.11'
Expand Down Expand Up @@ -208,13 +209,13 @@ dependencies {

compile 'org.jgrapht:jgrapht-core:0.9.1'
compile 'org.testng:testng:' + testNGVersion //compile instead of testCompile because it is needed for test infrastructure that needs to be packaged
compile 'org.apache.hadoop:hadoop-minicluster:2.7.2' //the version of minicluster should match the version of hadoop
compile 'org.apache.hadoop:hadoop-minicluster:' + hadoopVersion

compile('org.seqdoop:hadoop-bam:' + hadoopBamVersion) {
exclude group: 'org.apache.hadoop'
exclude module: 'htsjdk'
}
compile('org.apache.hadoop:hadoop-client:2.7.2') // should be a 'provided' dependency
compile('org.apache.hadoop:hadoop-client:' + hadoopVersion) // should be a 'provided' dependency
compile('com.github.jsr203hadoop:jsr203hadoop:1.0.3')

compile('de.javakaffee:kryo-serializers:0.41') {
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportColumn.java
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Expand Up @@ -66,7 +66,7 @@ public GATKReportColumnFormat getColumnFormat() {
* @return true if the value is a right alignable
*/
protected static boolean isRightAlign(final String value) {
return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value.trim());
return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isCreatable(value.trim());
}

/**
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