Update all our dependencies to the latest version (#1901)

build.gradle

@@ -59,23 +59,26 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.1')
+final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.5')
 dependencies {
- implementation('com.intel.gkl:gkl:0.8.8') {
+ implementation('com.intel.gkl:gkl:0.8.11') {
  exclude module: 'htsjdk'
  }
+ implementation 'org.broadinstitute:gatk-native-bindings:1.0.0' //this should be redundant when GKL is updated past 0.8.11
+
  implementation 'com.google.guava:guava:32.1.1-jre'
- implementation 'org.apache.commons:commons-math3:3.5'
- implementation 'org.apache.commons:commons-collections4:4.3'
+ implementation 'org.apache.commons:commons-math3:3.6.1'
+ implementation 'org.apache.commons:commons-collections4:4.4'
  implementation 'com.github.samtools:htsjdk:' + htsjdkVersion
  implementation 'org.broadinstitute:barclay:5.0.0'
- implementation 'org.apache.logging.log4j:log4j-api:2.17.1'
- implementation 'org.apache.logging.log4j:log4j-core:2.17.1'
+ implementation 'org.apache.logging.log4j:log4j-api:2.20.0'
+ implementation 'org.apache.logging.log4j:log4j-core:2.20.0'
  implementation 'org.openjdk.nashorn:nashorn-core:15.4'
- implementation 'org.apache.commons:commons-lang3:3.6'
+ implementation 'org.apache.commons:commons-lang3:3.12.0'
  implementation 'com.google.cloud:google-cloud-nio:0.127.0'
+ implementation 'commons-io:commons-io:2.11.0'
 
- testImplementation 'org.testng:testng:6.14.3'
+ testImplementation 'org.testng:testng:7.7.0'
 }
 
 configurations.all {