diff --git a/.idea/libraries/Maven__ch_qos_logback_logback_core_1_1_7.xml b/.idea/libraries/Maven__ch_qos_logback_logback_core_1_1_7.xml
deleted file mode 100644
index 6c2a7607..00000000
--- a/.idea/libraries/Maven__ch_qos_logback_logback_core_1_1_7.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__colt_colt_1_2_0.xml b/.idea/libraries/Maven__colt_colt_1_2_0.xml
deleted file mode 100644
index 58562acd..00000000
--- a/.idea/libraries/Maven__colt_colt_1_2_0.xml
+++ /dev/null
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deleted file mode 100644
index f0f9060d..00000000
--- a/.idea/libraries/Maven__com_beust_jcommander_1_27.xml
+++ /dev/null
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_github_lucarosellini_rJava_JRI_0_9_7.xml b/.idea/libraries/Maven__com_github_lucarosellini_rJava_JRI_0_9_7.xml
deleted file mode 100644
index 1ef9b54f..00000000
--- a/.idea/libraries/Maven__com_github_lucarosellini_rJava_JRI_0_9_7.xml
+++ /dev/null
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diff --git a/.idea/libraries/Maven__com_github_samtools_htsjdk_2_2_4.xml b/.idea/libraries/Maven__com_github_samtools_htsjdk_2_2_4.xml
deleted file mode 100644
index ed8df976..00000000
--- a/.idea/libraries/Maven__com_github_samtools_htsjdk_2_2_4.xml
+++ /dev/null
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\ No newline at end of file
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deleted file mode 100644
index 8ae2de12..00000000
--- a/.idea/libraries/Maven__com_google_guava_guava_15_0.xml
+++ /dev/null
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diff --git a/.idea/libraries/Maven__com_ibm_icu_icu4j_3_4_4.xml b/.idea/libraries/Maven__com_ibm_icu_icu4j_3_4_4.xml
deleted file mode 100644
index 5fb7b210..00000000
--- a/.idea/libraries/Maven__com_ibm_icu_icu4j_3_4_4.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_martiansoftware_jsap_2_1_2.xml b/.idea/libraries/Maven__com_martiansoftware_jsap_2_1_2.xml
deleted file mode 100644
index 13878dfe..00000000
--- a/.idea/libraries/Maven__com_martiansoftware_jsap_2_1_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__com_thoughtworks_xstream_xstream_1_4_8.xml b/.idea/libraries/Maven__com_thoughtworks_xstream_xstream_1_4_8.xml
deleted file mode 100644
index 46243f0d..00000000
--- a/.idea/libraries/Maven__com_thoughtworks_xstream_xstream_1_4_8.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_beanutils_commons_beanutils_1_8_3.xml b/.idea/libraries/Maven__commons_beanutils_commons_beanutils_1_8_3.xml
deleted file mode 100644
index 52b553d6..00000000
--- a/.idea/libraries/Maven__commons_beanutils_commons_beanutils_1_8_3.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_io_commons_io_2_3.xml b/.idea/libraries/Maven__commons_io_commons_io_2_3.xml
deleted file mode 100644
index df8396dd..00000000
--- a/.idea/libraries/Maven__commons_io_commons_io_2_3.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__commons_lang_commons_lang_2_4.xml b/.idea/libraries/Maven__commons_lang_commons_lang_2_4.xml
deleted file mode 100644
index 5e8b8d33..00000000
--- a/.idea/libraries/Maven__commons_lang_commons_lang_2_4.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml b/.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml
deleted file mode 100644
index 4acbd2f6..00000000
--- a/.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml
+++ /dev/null
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diff --git a/.idea/libraries/Maven__gov_nih_nlm_ncbi_ngs_java_1_2_2.xml b/.idea/libraries/Maven__gov_nih_nlm_ncbi_ngs_java_1_2_2.xml
deleted file mode 100644
index 9f3d4089..00000000
--- a/.idea/libraries/Maven__gov_nih_nlm_ncbi_ngs_java_1_2_2.xml
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diff --git a/.idea/libraries/Maven__log4j_log4j_1_2_16.xml b/.idea/libraries/Maven__log4j_log4j_1_2_16.xml
deleted file mode 100644
index 11837b5f..00000000
--- a/.idea/libraries/Maven__log4j_log4j_1_2_16.xml
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diff --git a/.idea/libraries/Maven__org_apache_ant_ant_1_8_2.xml b/.idea/libraries/Maven__org_apache_ant_ant_1_8_2.xml
deleted file mode 100644
index 5bdad071..00000000
--- a/.idea/libraries/Maven__org_apache_ant_ant_1_8_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_apache_ant_ant_launcher_1_8_2.xml b/.idea/libraries/Maven__org_apache_ant_ant_launcher_1_8_2.xml
deleted file mode 100644
index b810f735..00000000
--- a/.idea/libraries/Maven__org_apache_ant_ant_launcher_1_8_2.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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diff --git a/.idea/libraries/Maven__org_apache_commons_commons_compress_1_4_1.xml b/.idea/libraries/Maven__org_apache_commons_commons_compress_1_4_1.xml
deleted file mode 100644
index 190209ed..00000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_compress_1_4_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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diff --git a/.idea/libraries/Maven__org_apache_commons_commons_jexl_2_1_1.xml b/.idea/libraries/Maven__org_apache_commons_commons_jexl_2_1_1.xml
deleted file mode 100644
index fbbed3d8..00000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_jexl_2_1_1.xml
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diff --git a/.idea/libraries/Maven__org_apache_commons_commons_math3_3_0.xml b/.idea/libraries/Maven__org_apache_commons_commons_math3_3_0.xml
deleted file mode 100644
index 6aa47229..00000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_math3_3_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
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diff --git a/.idea/libraries/Maven__org_apache_commons_commons_math_2_2.xml b/.idea/libraries/Maven__org_apache_commons_commons_math_2_2.xml
deleted file mode 100644
index 8f3e3159..00000000
--- a/.idea/libraries/Maven__org_apache_commons_commons_math_2_2.xml
+++ /dev/null
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diff --git a/.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml b/.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml
deleted file mode 100644
index d6f17aa7..00000000
--- a/.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: org.beanshell:bsh:2.0b4">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/beanshell/bsh/2.0b4/bsh-2.0b4-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/beanshell/bsh/2.0b4/bsh-2.0b4-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_campagnelab_goby_goby_io_3_0_1.xml b/.idea/libraries/Maven__org_campagnelab_goby_goby_io_3_0_2.xml
similarity index 64%
rename from .idea/libraries/Maven__org_campagnelab_goby_goby_io_3_0_1.xml
rename to .idea/libraries/Maven__org_campagnelab_goby_goby_io_3_0_2.xml
index bd6eae19..67beeeba 100644
--- a/.idea/libraries/Maven__org_campagnelab_goby_goby_io_3_0_1.xml
+++ b/.idea/libraries/Maven__org_campagnelab_goby_goby_io_3_0_2.xml
@@ -1,13 +1,13 @@
 <component name="libraryTable">
-  <library name="Maven: org.campagnelab.goby:goby-io:3.0.1">
+  <library name="Maven: org.campagnelab.goby:goby-io:3.0.2">
     <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/goby/goby-io/3.0.1/goby-io-3.0.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/goby/goby-io/3.0.2/goby-io-3.0.2.jar!/" />
     </CLASSES>
     <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/goby/goby-io/3.0.1/goby-io-3.0.1-javadoc.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/goby/goby-io/3.0.2/goby-io-3.0.2-javadoc.jar!/" />
     </JAVADOC>
     <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/goby/goby-io/3.0.1/goby-io-3.0.1-sources.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/goby/goby-io/3.0.2/goby-io-3.0.2-sources.jar!/" />
     </SOURCES>
   </library>
 </component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_campagnelab_icb_icb_utils_2_0_0.xml b/.idea/libraries/Maven__org_campagnelab_icb_icb_utils_2_0_0.xml
deleted file mode 100644
index 42f0825d..00000000
--- a/.idea/libraries/Maven__org_campagnelab_icb_icb_utils_2_0_0.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: org.campagnelab.icb:icb-utils:2.0.0">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/icb/icb-utils/2.0.0/icb-utils-2.0.0.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/icb/icb-utils/2.0.0/icb-utils-2.0.0-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/campagnelab/icb/icb-utils/2.0.0/icb-utils-2.0.0-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_javassist_javassist_3_19_0_GA.xml b/.idea/libraries/Maven__org_javassist_javassist_3_19_0_GA.xml
deleted file mode 100644
index be983fcc..00000000
--- a/.idea/libraries/Maven__org_javassist_javassist_3_19_0_GA.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: org.javassist:javassist:3.19.0-GA">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/javassist/javassist/3.19.0-GA/javassist-3.19.0-GA.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/javassist/javassist/3.19.0-GA/javassist-3.19.0-GA-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/javassist/javassist/3.19.0-GA/javassist-3.19.0-GA-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_slf4j_slf4j_api_1_7_21.xml b/.idea/libraries/Maven__org_slf4j_slf4j_api_1_7_21.xml
deleted file mode 100644
index 1b644dd8..00000000
--- a/.idea/libraries/Maven__org_slf4j_slf4j_api_1_7_21.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: org.slf4j:slf4j-api:1.7.21">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.7.21/slf4j-api-1.7.21.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.7.21/slf4j-api-1.7.21-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.7.21/slf4j-api-1.7.21-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_testng_testng_6_8_8.xml b/.idea/libraries/Maven__org_testng_testng_6_8_8.xml
deleted file mode 100644
index 9ea815ac..00000000
--- a/.idea/libraries/Maven__org_testng_testng_6_8_8.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: org.testng:testng:6.8.8">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8.8/testng-6.8.8.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8.8/testng-6.8.8-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8.8/testng-6.8.8-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml b/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml
deleted file mode 100644
index dd59ad3b..00000000
--- a/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__xmlpull_xmlpull_1_1_3_1.xml b/.idea/libraries/Maven__xmlpull_xmlpull_1_1_3_1.xml
deleted file mode 100644
index 0f2d9ef4..00000000
--- a/.idea/libraries/Maven__xmlpull_xmlpull_1_1_3_1.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: xmlpull:xmlpull:1.1.3.1">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/xmlpull/xmlpull/1.1.3.1/xmlpull-1.1.3.1.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/xmlpull/xmlpull/1.1.3.1/xmlpull-1.1.3.1-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/xmlpull/xmlpull/1.1.3.1/xmlpull-1.1.3.1-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/Maven__xpp3_xpp3_min_1_1_4c.xml b/.idea/libraries/Maven__xpp3_xpp3_min_1_1_4c.xml
deleted file mode 100644
index 6726a2d6..00000000
--- a/.idea/libraries/Maven__xpp3_xpp3_min_1_1_4c.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="Maven: xpp3:xpp3_min:1.1.4c">
-    <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar!/" />
-    </CLASSES>
-    <JAVADOC>
-      <root url="jar://$MAVEN_REPOSITORY$/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c-javadoc.jar!/" />
-    </JAVADOC>
-    <SOURCES>
-      <root url="jar://$MAVEN_REPOSITORY$/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c-sources.jar!/" />
-    </SOURCES>
-  </library>
-</component>
\ No newline at end of file
diff --git a/VariationAnalysis.iml b/VariationAnalysis.iml
index da8ee76e..10cf23e4 100644
--- a/VariationAnalysis.iml
+++ b/VariationAnalysis.iml
@@ -38,45 +38,6 @@
         <SOURCES />
       </library>
     </orderEntry>
-    <orderEntry type="library" name="Maven: org.campagnelab.goby:goby-io:3.0.1" level="project" />
-    <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:7.0.12" level="project" />
-    <orderEntry type="library" name="Maven: org.campagnelab.icb:icb-utils:2.0.0" level="project" />
-    <orderEntry type="library" name="Maven: com.ibm.icu:icu4j:3.4.4" level="project" />
-    <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.4" level="project" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.3" level="project" />
-    <orderEntry type="library" name="Maven: commons-beanutils:commons-beanutils:1.8.3" level="project" />
-    <orderEntry type="library" name="Maven: com.martiansoftware:jsap:2.1.2" level="project" />
-    <orderEntry type="library" name="Maven: com.thoughtworks.xstream:xstream:1.4.8" level="project" />
-    <orderEntry type="library" name="Maven: xmlpull:xmlpull:1.1.3.1" level="project" />
-    <orderEntry type="library" name="Maven: xpp3:xpp3_min:1.1.4c" level="project" />
-    <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
-    <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-math3:3.0" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.16" level="project" />
-    <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.7.21" level="project" />
-    <orderEntry type="library" name="Maven: it.unimi.dsi:dsiutils:2.3.3" level="project" />
-    <orderEntry type="library" name="Maven: ch.qos.logback:logback-classic:1.1.7" level="project" />
-    <orderEntry type="library" name="Maven: ch.qos.logback:logback-core:1.1.7" level="project" />
-    <orderEntry type="library" name="Maven: commons-configuration:commons-configuration:1.10" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:20040616" level="project" />
-    <orderEntry type="library" name="Maven: com.github.samtools:htsjdk:2.2.4" level="project" />
-    <orderEntry type="library" name="Maven: gov.nih.nlm.ncbi:ngs-java:1.2.2" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
-    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
-    <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-compress:1.4.1" level="project" />
-    <orderEntry type="library" name="Maven: org.tukaani:xz:1.5" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.ant:ant-launcher:1.8.2" level="project" />
-    <orderEntry type="library" name="Maven: org.testng:testng:6.8.8" level="project" />
-    <orderEntry type="library" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
-    <orderEntry type="library" name="Maven: com.beust:jcommander:1.27" level="project" />
-    <orderEntry type="library" name="Maven: com.google.protobuf:protobuf-java:3.0.0-beta-4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.10" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:15.0" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.19.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:annotations:2.0.1" level="project" />
-    <orderEntry type="library" name="Maven: com.github.lucarosellini.rJava:JRI:0.9-7" level="project" />
+    <orderEntry type="library" name="Maven: org.campagnelab.goby:goby-io:3.0.2" level="project" />
   </component>
 </module>
\ No newline at end of file
diff --git a/model-training/model-training.iml b/model-training/model-training.iml
index 226b5e32..2bc3a977 100644
--- a/model-training/model-training.iml
+++ b/model-training/model-training.iml
@@ -38,6 +38,8 @@
     <orderEntry type="library" name="Maven: org.nd4j:nd4j-api:0.5.0" level="project" />
     <orderEntry type="library" name="Maven: org.nd4j:nd4j-buffer:0.5.0" level="project" />
     <orderEntry type="library" name="Maven: org.nd4j:nd4j-common:0.5.0" level="project" />
+    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.10" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.findbugs:annotations:2.0.1" level="project" />
     <orderEntry type="library" name="Maven: org.nd4j:nd4j-context:0.5.0" level="project" />
     <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.3.1" level="project" />
     <orderEntry type="library" name="Maven: com.fasterxml.jackson.core:jackson-core:2.5.1" level="project" />
@@ -170,6 +172,7 @@
     <orderEntry type="library" name="Maven: org.glassfish.hk2.external:aopalliance-repackaged:2.4.0-b09" level="project" />
     <orderEntry type="library" name="Maven: org.glassfish.hk2.external:javax.inject:2.4.0-b09" level="project" />
     <orderEntry type="library" name="Maven: org.glassfish.hk2:hk2-locator:2.4.0-b09" level="project" />
+    <orderEntry type="library" name="Maven: org.javassist:javassist:3.18.1-GA" level="project" />
     <orderEntry type="library" name="Maven: io.dropwizard.metrics:metrics-httpclient:3.1.0" level="project" />
     <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.3.5" level="project" />
     <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.3.2" level="project" />
@@ -196,25 +199,6 @@
     <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
     <orderEntry type="library" name="Maven: commons-collections:commons-collections:20040616" level="project" />
     <orderEntry type="library" name="Maven: com.beust:jcommander:1.48" level="project" />
-    <orderEntry type="library" name="Maven: org.campagnelab.goby:goby-io:3.0.1" level="project" />
-    <orderEntry type="library" name="Maven: org.campagnelab.icb:icb-utils:2.0.0" level="project" />
-    <orderEntry type="library" name="Maven: com.ibm.icu:icu4j:3.4.4" level="project" />
-    <orderEntry type="library" name="Maven: commons-beanutils:commons-beanutils:1.8.3" level="project" />
-    <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
-    <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.16" level="project" />
-    <orderEntry type="library" name="Maven: com.github.samtools:htsjdk:2.2.4" level="project" />
-    <orderEntry type="library" name="Maven: gov.nih.nlm.ncbi:ngs-java:1.2.2" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
-    <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.ant:ant-launcher:1.8.2" level="project" />
-    <orderEntry type="library" name="Maven: org.testng:testng:6.8.8" level="project" />
-    <orderEntry type="library" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.10" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.19.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:annotations:2.0.1" level="project" />
-    <orderEntry type="library" name="Maven: com.github.lucarosellini.rJava:JRI:0.9-7" level="project" />
+    <orderEntry type="library" name="Maven: org.campagnelab.goby:goby-io:3.0.2" level="project" />
   </component>
 </module>
\ No newline at end of file
diff --git a/model-utils/model-utils.iml b/model-utils/model-utils.iml
index 90a8ca51..51ca7432 100644
--- a/model-utils/model-utils.iml
+++ b/model-utils/model-utils.iml
@@ -190,5 +190,6 @@
     <orderEntry type="library" name="Maven: org.nd4j:nd4j-native-api:0.5.0" level="project" />
     <orderEntry type="library" name="Maven: com.google.protobuf:protobuf-java:3.0.0-beta-4" level="project" />
     <orderEntry type="library" name="Maven: com.beust:jcommander:1.48" level="project" />
+    <orderEntry type="library" name="Maven: org.campagnelab.goby:goby-io:3.0.2" level="project" />
   </component>
 </module>
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 1c04d1c7..55af988a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -123,11 +123,11 @@
             </snapshots>
         </repository>
         <!-- nexus staging can be used to test staged artifacts before their official release -->
-        <!--repository>
+        <repository>
             <id>nexus-staging</id>
             <name>Nexus Release Repository</name>
             <url>https://oss.sonatype.org/content/groups/staging</url>
-        </repository-->
+        </repository>
     </repositories>
 
     <distributionManagement>
@@ -147,7 +147,7 @@
         <dependency>
             <groupId>org.campagnelab.goby</groupId>
             <artifactId>goby-io</artifactId>
-            <version>3.0.1</version>
+            <version>3.0.2</version>
         </dependency>
     </dependencies>