Remove adam- prefix from module directory names.

bigdatagenomics · Aug 24, 2017 · f1cd684 · f1cd684
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commit f1cd684
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Showing 452 changed files with 36 additions and 36 deletions.
diff --git a/adam-cli/src/test/resources/artificial.fa b/adam-cli/src/test/resources/artificial.fa
diff --git a/adam-cli/src/test/resources/artificial.fa.fai b/adam-cli/src/test/resources/artificial.fa.fai
diff --git a/adam-apis/pom.xml → apis/pom.xml b/adam-apis/pom.xml → apis/pom.xml
diff --git a/...m/api/java/GenomicDatasetConverters.scala → ...m/api/java/GenomicDatasetConverters.scala b/...m/api/java/GenomicDatasetConverters.scala → ...m/api/java/GenomicDatasetConverters.scala
diff --git a/.../adam/api/java/GenomicRDDConverters.scala → .../adam/api/java/GenomicRDDConverters.scala b/.../adam/api/java/GenomicRDDConverters.scala → .../adam/api/java/GenomicRDDConverters.scala
diff --git a/...omics/adam/api/java/JavaADAMContext.scala → ...omics/adam/api/java/JavaADAMContext.scala b/...omics/adam/api/java/JavaADAMContext.scala → ...omics/adam/api/java/JavaADAMContext.scala
diff --git a/...i/python/DataFrameConversionWrapper.scala → ...i/python/DataFrameConversionWrapper.scala b/...i/python/DataFrameConversionWrapper.scala → ...i/python/DataFrameConversionWrapper.scala
diff --git a/.../adam/api/java/JavaADAMContigConduit.java → .../adam/api/java/JavaADAMContigConduit.java b/.../adam/api/java/JavaADAMContigConduit.java → .../adam/api/java/JavaADAMContigConduit.java
diff --git a/...dam/api/java/JavaADAMCoverageConduit.java → ...dam/api/java/JavaADAMCoverageConduit.java b/...dam/api/java/JavaADAMCoverageConduit.java → ...dam/api/java/JavaADAMCoverageConduit.java
diff --git a/...adam/api/java/JavaADAMFeatureConduit.java → ...adam/api/java/JavaADAMFeatureConduit.java b/...adam/api/java/JavaADAMFeatureConduit.java → ...adam/api/java/JavaADAMFeatureConduit.java
diff --git a/...dam/api/java/JavaADAMFragmentConduit.java → ...dam/api/java/JavaADAMFragmentConduit.java b/...dam/api/java/JavaADAMFragmentConduit.java → ...dam/api/java/JavaADAMFragmentConduit.java
diff --git a/...dam/api/java/JavaADAMGenotypeConduit.java → ...dam/api/java/JavaADAMGenotypeConduit.java b/...dam/api/java/JavaADAMGenotypeConduit.java → ...dam/api/java/JavaADAMGenotypeConduit.java
diff --git a/...cs/adam/api/java/JavaADAMReadConduit.java → ...cs/adam/api/java/JavaADAMReadConduit.java b/...cs/adam/api/java/JavaADAMReadConduit.java → ...cs/adam/api/java/JavaADAMReadConduit.java
diff --git a/...adam/api/java/JavaADAMVariantConduit.java → ...adam/api/java/JavaADAMVariantConduit.java b/...adam/api/java/JavaADAMVariantConduit.java → ...adam/api/java/JavaADAMVariantConduit.java
diff --git a/.../adam/api/java/JavaADAMContextSuite.scala → .../adam/api/java/JavaADAMContextSuite.scala b/.../adam/api/java/JavaADAMContextSuite.scala → .../adam/api/java/JavaADAMContextSuite.scala
diff --git a/adam-assembly/pom.xml → assembly/pom.xml b/adam-assembly/pom.xml → assembly/pom.xml
diff --git a/...g/bdgenomics/adam/assembly/Assembly.scala → ...g/bdgenomics/adam/assembly/Assembly.scala b/...g/bdgenomics/adam/assembly/Assembly.scala → ...g/bdgenomics/adam/assembly/Assembly.scala
diff --git a/bin/adam-shell b/bin/adam-shell
@@ -41,7 +41,7 @@ ADAM_CLI_JAR=
 if [ -d "$INSTALL_DIR/repo" ]; then
   ASSEMBLY_DIR="$INSTALL_DIR/repo"
 else
-  ASSEMBLY_DIR="$INSTALL_DIR/adam-assembly/target"
+  ASSEMBLY_DIR="$INSTALL_DIR/assembly/target"
 fi
 
 num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\.\_\-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)"

diff --git a/bin/adam-submit b/bin/adam-submit
@@ -65,7 +65,7 @@ ADAM_CLI_JAR=
 if [ -d "$INSTALL_DIR/repo" ]; then
   ASSEMBLY_DIR="$INSTALL_DIR/repo"
 else
-  ASSEMBLY_DIR="$INSTALL_DIR/adam-assembly/target"
+  ASSEMBLY_DIR="$INSTALL_DIR/assembly/target"
 fi
 
 num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\.\_\-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)"

diff --git a/bin/pyadam b/bin/pyadam
@@ -27,7 +27,7 @@ ADAM_CLI_JAR=
 if [ -d "$SCRIPT_DIR/repo" ]; then
   ASSEMBLY_DIR="$SCRIPT_DIR/repo"
 else
-  ASSEMBLY_DIR="$SCRIPT_DIR/adam-assembly/target"
+  ASSEMBLY_DIR="$SCRIPT_DIR/assembly/target"
 fi
 
 num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)"

diff --git a/adam-cli/.gitignore → cli/.gitignore b/adam-cli/.gitignore → cli/.gitignore
diff --git a/adam-cli/pom.xml → cli/pom.xml b/adam-cli/pom.xml → cli/pom.xml
diff --git a/...plates/org/bdgenomics/adam/cli/About.java → ...plates/org/bdgenomics/adam/cli/About.java b/...plates/org/bdgenomics/adam/cli/About.java → ...plates/org/bdgenomics/adam/cli/About.java
diff --git a/.../org/bdgenomics/adam/cli/ADAM2Fasta.scala → .../org/bdgenomics/adam/cli/ADAM2Fasta.scala b/.../org/bdgenomics/adam/cli/ADAM2Fasta.scala → .../org/bdgenomics/adam/cli/ADAM2Fasta.scala
diff --git a/.../org/bdgenomics/adam/cli/ADAM2Fastq.scala → .../org/bdgenomics/adam/cli/ADAM2Fastq.scala b/.../org/bdgenomics/adam/cli/ADAM2Fastq.scala → .../org/bdgenomics/adam/cli/ADAM2Fastq.scala
diff --git a/...la/org/bdgenomics/adam/cli/ADAMMain.scala → ...la/org/bdgenomics/adam/cli/ADAMMain.scala b/...la/org/bdgenomics/adam/cli/ADAMMain.scala → ...la/org/bdgenomics/adam/cli/ADAMMain.scala
diff --git a/...dgenomics/adam/cli/CountContigKmers.scala → ...dgenomics/adam/cli/CountContigKmers.scala b/...dgenomics/adam/cli/CountContigKmers.scala → ...dgenomics/adam/cli/CountContigKmers.scala
diff --git a/.../bdgenomics/adam/cli/CountReadKmers.scala → .../bdgenomics/adam/cli/CountReadKmers.scala b/.../bdgenomics/adam/cli/CountReadKmers.scala → .../bdgenomics/adam/cli/CountReadKmers.scala
diff --git a/.../org/bdgenomics/adam/cli/Fasta2ADAM.scala → .../org/bdgenomics/adam/cli/Fasta2ADAM.scala b/.../org/bdgenomics/adam/cli/Fasta2ADAM.scala → .../org/bdgenomics/adam/cli/Fasta2ADAM.scala
diff --git a/...la/org/bdgenomics/adam/cli/FlagStat.scala → ...la/org/bdgenomics/adam/cli/FlagStat.scala b/...la/org/bdgenomics/adam/cli/FlagStat.scala → ...la/org/bdgenomics/adam/cli/FlagStat.scala
diff --git a/...org/bdgenomics/adam/cli/MergeShards.scala → ...org/bdgenomics/adam/cli/MergeShards.scala b/...org/bdgenomics/adam/cli/MergeShards.scala → ...org/bdgenomics/adam/cli/MergeShards.scala
diff --git a/...a/org/bdgenomics/adam/cli/PrintADAM.scala → ...a/org/bdgenomics/adam/cli/PrintADAM.scala b/...a/org/bdgenomics/adam/cli/PrintADAM.scala → ...a/org/bdgenomics/adam/cli/PrintADAM.scala
diff --git a/.../bdgenomics/adam/cli/Reads2Coverage.scala → .../bdgenomics/adam/cli/Reads2Coverage.scala b/.../bdgenomics/adam/cli/Reads2Coverage.scala → .../bdgenomics/adam/cli/Reads2Coverage.scala
diff --git a/...nomics/adam/cli/TransformAlignments.scala → ...nomics/adam/cli/TransformAlignments.scala b/...nomics/adam/cli/TransformAlignments.scala → ...nomics/adam/cli/TransformAlignments.scala
diff --git a/...genomics/adam/cli/TransformFeatures.scala → ...genomics/adam/cli/TransformFeatures.scala b/...genomics/adam/cli/TransformFeatures.scala → ...genomics/adam/cli/TransformFeatures.scala
diff --git a/...enomics/adam/cli/TransformFragments.scala → ...enomics/adam/cli/TransformFragments.scala b/...enomics/adam/cli/TransformFragments.scala → ...enomics/adam/cli/TransformFragments.scala
diff --git a/...enomics/adam/cli/TransformGenotypes.scala → ...enomics/adam/cli/TransformGenotypes.scala b/...enomics/adam/cli/TransformGenotypes.scala → ...enomics/adam/cli/TransformGenotypes.scala
diff --git a/...genomics/adam/cli/TransformVariants.scala → ...genomics/adam/cli/TransformVariants.scala b/...genomics/adam/cli/TransformVariants.scala → ...genomics/adam/cli/TransformVariants.scala
diff --git a/.../scala/org/bdgenomics/adam/cli/View.scala → .../scala/org/bdgenomics/adam/cli/View.scala b/.../scala/org/bdgenomics/adam/cli/View.scala → .../scala/org/bdgenomics/adam/cli/View.scala
diff --git a/cli/src/test/resources/artificial.fa b/cli/src/test/resources/artificial.fa
@@ -0,0 +1 @@
+../../../../core/src/test/resources/artificial.fa
diff --git a/cli/src/test/resources/artificial.fa.fai b/cli/src/test/resources/artificial.fa.fai
@@ -0,0 +1 @@
+../../../../core/src/test/resources/artificial.fa.fai
diff --git a/adam-cli/src/test/resources/bqsr1-r1.fq → cli/src/test/resources/bqsr1-r1.fq b/adam-cli/src/test/resources/bqsr1-r1.fq → cli/src/test/resources/bqsr1-r1.fq
diff --git a/adam-cli/src/test/resources/bqsr1-r2.fq → cli/src/test/resources/bqsr1-r2.fq b/adam-cli/src/test/resources/bqsr1-r2.fq → cli/src/test/resources/bqsr1-r2.fq
diff --git a/adam-cli/src/test/resources/bqsr1.sam → cli/src/test/resources/bqsr1.sam b/adam-cli/src/test/resources/bqsr1.sam → cli/src/test/resources/bqsr1.sam
diff --git a/...t/resources/chr5.phyloP46way.trunc.wigFix → ...t/resources/chr5.phyloP46way.trunc.wigFix b/...t/resources/chr5.phyloP46way.trunc.wigFix → ...t/resources/chr5.phyloP46way.trunc.wigFix
diff --git a/adam-cli/src/test/resources/contigs.fa → cli/src/test/resources/contigs.fa b/adam-cli/src/test/resources/contigs.fa → cli/src/test/resources/contigs.fa
diff --git a/adam-cli/src/test/resources/flag-values.sam → cli/src/test/resources/flag-values.sam b/adam-cli/src/test/resources/flag-values.sam → cli/src/test/resources/flag-values.sam
diff --git a/...sources/gencode.v7.annotation.trunc10.bed → ...sources/gencode.v7.annotation.trunc10.bed b/...sources/gencode.v7.annotation.trunc10.bed → ...sources/gencode.v7.annotation.trunc10.bed
diff --git a/adam-cli/src/test/resources/log4j.properties → cli/src/test/resources/log4j.properties b/adam-cli/src/test/resources/log4j.properties → cli/src/test/resources/log4j.properties
diff --git a/adam-cli/src/test/resources/small.vcf → cli/src/test/resources/small.vcf b/adam-cli/src/test/resources/small.vcf → cli/src/test/resources/small.vcf
diff --git a/adam-cli/src/test/resources/sorted.bam → cli/src/test/resources/sorted.bam b/adam-cli/src/test/resources/sorted.bam → cli/src/test/resources/sorted.bam
diff --git a/adam-cli/src/test/resources/sorted.bam.bai → cli/src/test/resources/sorted.bam.bai b/adam-cli/src/test/resources/sorted.bam.bai → cli/src/test/resources/sorted.bam.bai
diff --git a/...bdgenomics/adam/cli/ADAM2FastaSuite.scala → ...bdgenomics/adam/cli/ADAM2FastaSuite.scala b/...bdgenomics/adam/cli/ADAM2FastaSuite.scala → ...bdgenomics/adam/cli/ADAM2FastaSuite.scala
diff --git a/...bdgenomics/adam/cli/ADAM2FastqSuite.scala → ...bdgenomics/adam/cli/ADAM2FastqSuite.scala b/...bdgenomics/adam/cli/ADAM2FastqSuite.scala → ...bdgenomics/adam/cli/ADAM2FastqSuite.scala
diff --git a/...g/bdgenomics/adam/cli/ADAMMainSuite.scala → ...g/bdgenomics/adam/cli/ADAMMainSuite.scala b/...g/bdgenomics/adam/cli/ADAMMainSuite.scala → ...g/bdgenomics/adam/cli/ADAMMainSuite.scala
diff --git a/.../org/bdgenomics/adam/cli/AboutSuite.scala → .../org/bdgenomics/adam/cli/AboutSuite.scala b/.../org/bdgenomics/adam/cli/AboutSuite.scala → .../org/bdgenomics/adam/cli/AboutSuite.scala
diff --git a/...bdgenomics/adam/cli/Fasta2ADAMSuite.scala → ...bdgenomics/adam/cli/Fasta2ADAMSuite.scala b/...bdgenomics/adam/cli/Fasta2ADAMSuite.scala → ...bdgenomics/adam/cli/Fasta2ADAMSuite.scala
diff --git a/...dgenomics/adam/cli/MergeShardsSuite.scala → ...dgenomics/adam/cli/MergeShardsSuite.scala b/...dgenomics/adam/cli/MergeShardsSuite.scala → ...dgenomics/adam/cli/MergeShardsSuite.scala
diff --git a/...g/bdgenomics/adam/cli/ParquetLister.scala → ...g/bdgenomics/adam/cli/ParquetLister.scala b/...g/bdgenomics/adam/cli/ParquetLister.scala → ...g/bdgenomics/adam/cli/ParquetLister.scala
diff --git a/...nomics/adam/cli/Reads2CoverageSuite.scala → ...nomics/adam/cli/Reads2CoverageSuite.scala b/...nomics/adam/cli/Reads2CoverageSuite.scala → ...nomics/adam/cli/Reads2CoverageSuite.scala
diff --git a/...s/adam/cli/TransformAlignmentsSuite.scala → ...s/adam/cli/TransformAlignmentsSuite.scala b/...s/adam/cli/TransformAlignmentsSuite.scala → ...s/adam/cli/TransformAlignmentsSuite.scala
diff --git a/...ics/adam/cli/TransformFeaturesSuite.scala → ...ics/adam/cli/TransformFeaturesSuite.scala b/...ics/adam/cli/TransformFeaturesSuite.scala → ...ics/adam/cli/TransformFeaturesSuite.scala
diff --git a/...cs/adam/cli/TransformFragmentsSuite.scala → ...cs/adam/cli/TransformFragmentsSuite.scala b/...cs/adam/cli/TransformFragmentsSuite.scala → ...cs/adam/cli/TransformFragmentsSuite.scala
diff --git a/...cs/adam/cli/TransformGenotypesSuite.scala → ...cs/adam/cli/TransformGenotypesSuite.scala b/...cs/adam/cli/TransformGenotypesSuite.scala → ...cs/adam/cli/TransformGenotypesSuite.scala
diff --git a/...ics/adam/cli/TransformVariantsSuite.scala → ...ics/adam/cli/TransformVariantsSuite.scala b/...ics/adam/cli/TransformVariantsSuite.scala → ...ics/adam/cli/TransformVariantsSuite.scala
diff --git a/...a/org/bdgenomics/adam/cli/ViewSuite.scala → ...a/org/bdgenomics/adam/cli/ViewSuite.scala b/...a/org/bdgenomics/adam/cli/ViewSuite.scala → ...a/org/bdgenomics/adam/cli/ViewSuite.scala
diff --git a/adam-codegen/pom.xml → codegen/pom.xml b/adam-codegen/pom.xml → codegen/pom.xml
diff --git a/...s/adam/codegen/DumpSchemasToProduct.scala → ...s/adam/codegen/DumpSchemasToProduct.scala b/...s/adam/codegen/DumpSchemasToProduct.scala → ...s/adam/codegen/DumpSchemasToProduct.scala
diff --git a/...odegen/DumpSchemasToProjectionEnums.scala → ...odegen/DumpSchemasToProjectionEnums.scala b/...odegen/DumpSchemasToProjectionEnums.scala → ...odegen/DumpSchemasToProjectionEnums.scala
diff --git a/...g/bdgenomics/adam/codegen/Generator.scala → ...g/bdgenomics/adam/codegen/Generator.scala b/...g/bdgenomics/adam/codegen/Generator.scala → ...g/bdgenomics/adam/codegen/Generator.scala
diff --git a/...genomics/adam/codegen/ReflectSchema.scala → ...genomics/adam/codegen/ReflectSchema.scala b/...genomics/adam/codegen/ReflectSchema.scala → ...genomics/adam/codegen/ReflectSchema.scala
diff --git a/adam-core/.gitignore → core/.gitignore b/adam-core/.gitignore → core/.gitignore
diff --git a/adam-core/pom.xml → core/pom.xml b/adam-core/pom.xml → core/pom.xml
@@ -114,7 +114,7 @@
                 <argument>org.bdgenomics.formats.avro.Variant</argument>
                 <argument>org.bdgenomics.formats.avro.VariantAnnotation</argument>
                 <argument>org.bdgenomics.formats.avro.VariantCallingAnnotations</argument>
-                <argument>adam-core/target/generated-sources/src/main/scala/org/bdgenomics/adam/sql/Schemas.scala</argument>
+                <argument>core/target/generated-sources/src/main/scala/org/bdgenomics/adam/sql/Schemas.scala</argument>
               </arguments>
               <classpathScope>compile</classpathScope>
             </configuration>
@@ -146,7 +146,7 @@
                 <argument>org.bdgenomics.formats.avro.Variant</argument>
                 <argument>org.bdgenomics.formats.avro.VariantAnnotation</argument>
                 <argument>org.bdgenomics.formats.avro.VariantCallingAnnotations</argument>
-                <argument>adam-core/target/generated-sources/src/main/scala/org/bdgenomics/adam/projections/Enums.scala</argument>
+                <argument>core/target/generated-sources/src/main/scala/org/bdgenomics/adam/projections/Enums.scala</argument>
               </arguments>
               <classpathScope>compile</classpathScope>
             </configuration>

diff --git a/.../bdgenomics/adam/io/FastqInputFormat.java → .../bdgenomics/adam/io/FastqInputFormat.java b/.../bdgenomics/adam/io/FastqInputFormat.java → .../bdgenomics/adam/io/FastqInputFormat.java
diff --git a/...bdgenomics/adam/io/FastqRecordReader.java → ...bdgenomics/adam/io/FastqRecordReader.java b/...bdgenomics/adam/io/FastqRecordReader.java → ...bdgenomics/adam/io/FastqRecordReader.java
diff --git a/.../adam/io/InterleavedFastqInputFormat.java → .../adam/io/InterleavedFastqInputFormat.java b/.../adam/io/InterleavedFastqInputFormat.java → .../adam/io/InterleavedFastqInputFormat.java
diff --git a/.../ResettableCompressedSplitLineReader.java → .../ResettableCompressedSplitLineReader.java b/.../ResettableCompressedSplitLineReader.java → .../ResettableCompressedSplitLineReader.java
diff --git a/...omics/adam/io/SingleFastqInputFormat.java → ...omics/adam/io/SingleFastqInputFormat.java b/...omics/adam/io/SingleFastqInputFormat.java → ...omics/adam/io/SingleFastqInputFormat.java
diff --git a/...adam/algorithms/consensus/Consensus.scala → ...adam/algorithms/consensus/Consensus.scala b/...adam/algorithms/consensus/Consensus.scala → ...adam/algorithms/consensus/Consensus.scala
diff --git a/...rithms/consensus/ConsensusGenerator.scala → ...rithms/consensus/ConsensusGenerator.scala b/...rithms/consensus/ConsensusGenerator.scala → ...rithms/consensus/ConsensusGenerator.scala
diff --git a/...sensus/ConsensusGeneratorFromKnowns.scala → ...sensus/ConsensusGeneratorFromKnowns.scala b/...sensus/ConsensusGeneratorFromKnowns.scala → ...sensus/ConsensusGeneratorFromKnowns.scala
diff --git a/...nsensus/ConsensusGeneratorFromReads.scala → ...nsensus/ConsensusGeneratorFromReads.scala b/...nsensus/ConsensusGeneratorFromReads.scala → ...nsensus/ConsensusGeneratorFromReads.scala
diff --git a/...ConsensusGeneratorFromSmithWaterman.scala → ...ConsensusGeneratorFromSmithWaterman.scala b/...ConsensusGeneratorFromSmithWaterman.scala → ...ConsensusGeneratorFromSmithWaterman.scala
diff --git a/...rithms/consensus/NormalizationUtils.scala → ...rithms/consensus/NormalizationUtils.scala b/...rithms/consensus/NormalizationUtils.scala → ...rithms/consensus/NormalizationUtils.scala
diff --git a/...s/consensus/UnionConsensusGenerator.scala → ...s/consensus/UnionConsensusGenerator.scala b/...s/consensus/UnionConsensusGenerator.scala → ...s/consensus/UnionConsensusGenerator.scala
diff --git a/...orithms/smithwaterman/SmithWaterman.scala → ...orithms/smithwaterman/SmithWaterman.scala b/...orithms/smithwaterman/SmithWaterman.scala → ...orithms/smithwaterman/SmithWaterman.scala
diff --git a/...man/SmithWatermanConstantGapScoring.scala → ...man/SmithWatermanConstantGapScoring.scala b/...man/SmithWatermanConstantGapScoring.scala → ...man/SmithWatermanConstantGapScoring.scala
diff --git a/...erman/SmithWatermanGapScoringFromFn.scala → ...erman/SmithWatermanGapScoringFromFn.scala b/...erman/SmithWatermanGapScoringFromFn.scala → ...erman/SmithWatermanGapScoringFromFn.scala
diff --git a/...converters/AlignmentRecordConverter.scala → ...converters/AlignmentRecordConverter.scala b/...converters/AlignmentRecordConverter.scala → ...converters/AlignmentRecordConverter.scala
diff --git a/.../adam/converters/DefaultHeaderLines.scala → .../adam/converters/DefaultHeaderLines.scala b/.../adam/converters/DefaultHeaderLines.scala → .../adam/converters/DefaultHeaderLines.scala
diff --git a/...mics/adam/converters/FastaConverter.scala → ...mics/adam/converters/FastaConverter.scala b/...mics/adam/converters/FastaConverter.scala → ...mics/adam/converters/FastaConverter.scala
diff --git a/...dam/converters/FastqRecordConverter.scala → ...dam/converters/FastqRecordConverter.scala b/...dam/converters/FastqRecordConverter.scala → ...dam/converters/FastqRecordConverter.scala
diff --git a/...s/adam/converters/FragmentConverter.scala → ...s/adam/converters/FragmentConverter.scala b/...s/adam/converters/FragmentConverter.scala → ...s/adam/converters/FragmentConverter.scala
diff --git a/.../adam/converters/SAMRecordConverter.scala → .../adam/converters/SAMRecordConverter.scala b/.../adam/converters/SAMRecordConverter.scala → .../adam/converters/SAMRecordConverter.scala
diff --git a/...onverters/TranscriptEffectConverter.scala → ...onverters/TranscriptEffectConverter.scala b/...onverters/TranscriptEffectConverter.scala → ...onverters/TranscriptEffectConverter.scala
diff --git a/.../converters/VariantContextConverter.scala → .../converters/VariantContextConverter.scala b/.../converters/VariantContextConverter.scala → .../converters/VariantContextConverter.scala
diff --git a/...enomics/adam/instrumentation/Timers.scala → ...enomics/adam/instrumentation/Timers.scala b/...enomics/adam/instrumentation/Timers.scala → ...enomics/adam/instrumentation/Timers.scala
diff --git a/...org/bdgenomics/adam/models/Alphabet.scala → ...org/bdgenomics/adam/models/Alphabet.scala b/...org/bdgenomics/adam/models/Alphabet.scala → ...org/bdgenomics/adam/models/Alphabet.scala
diff --git a/...rg/bdgenomics/adam/models/Attribute.scala → ...rg/bdgenomics/adam/models/Attribute.scala b/...rg/bdgenomics/adam/models/Attribute.scala → ...rg/bdgenomics/adam/models/Attribute.scala
diff --git a/...org/bdgenomics/adam/models/Coverage.scala → ...org/bdgenomics/adam/models/Coverage.scala b/...org/bdgenomics/adam/models/Coverage.scala → ...org/bdgenomics/adam/models/Coverage.scala
diff --git a/...g/bdgenomics/adam/models/IndelTable.scala → ...g/bdgenomics/adam/models/IndelTable.scala b/...g/bdgenomics/adam/models/IndelTable.scala → ...g/bdgenomics/adam/models/IndelTable.scala
diff --git a/...la/org/bdgenomics/adam/models/MdTag.scala → ...la/org/bdgenomics/adam/models/MdTag.scala b/...la/org/bdgenomics/adam/models/MdTag.scala → ...la/org/bdgenomics/adam/models/MdTag.scala
diff --git a/...s/adam/models/NonoverlappingRegions.scala → ...s/adam/models/NonoverlappingRegions.scala b/...s/adam/models/NonoverlappingRegions.scala → ...s/adam/models/NonoverlappingRegions.scala
diff --git a/...s/adam/models/RecordGroupDictionary.scala → ...s/adam/models/RecordGroupDictionary.scala b/...s/adam/models/RecordGroupDictionary.scala → ...s/adam/models/RecordGroupDictionary.scala
diff --git a/...omics/adam/models/ReferencePosition.scala → ...omics/adam/models/ReferencePosition.scala b/...omics/adam/models/ReferencePosition.scala → ...omics/adam/models/ReferencePosition.scala
diff --git a/...enomics/adam/models/ReferenceRegion.scala → ...enomics/adam/models/ReferenceRegion.scala b/...enomics/adam/models/ReferenceRegion.scala → ...enomics/adam/models/ReferenceRegion.scala
diff --git a/...s/adam/models/SAMFileHeaderWritable.scala → ...s/adam/models/SAMFileHeaderWritable.scala b/...s/adam/models/SAMFileHeaderWritable.scala → ...s/adam/models/SAMFileHeaderWritable.scala
diff --git a/...mics/adam/models/SequenceDictionary.scala → ...mics/adam/models/SequenceDictionary.scala b/...mics/adam/models/SequenceDictionary.scala → ...mics/adam/models/SequenceDictionary.scala
diff --git a/...org/bdgenomics/adam/models/SnpTable.scala → ...org/bdgenomics/adam/models/SnpTable.scala b/...org/bdgenomics/adam/models/SnpTable.scala → ...org/bdgenomics/adam/models/SnpTable.scala
diff --git a/...omics/adam/models/VCFHeaderWritable.scala → ...omics/adam/models/VCFHeaderWritable.scala b/...omics/adam/models/VCFHeaderWritable.scala → ...omics/adam/models/VCFHeaderWritable.scala
diff --git a/...genomics/adam/models/VariantContext.scala → ...genomics/adam/models/VariantContext.scala b/...genomics/adam/models/VariantContext.scala → ...genomics/adam/models/VariantContext.scala
diff --git a/...s/adam/projections/FieldEnumeration.scala → ...s/adam/projections/FieldEnumeration.scala b/...s/adam/projections/FieldEnumeration.scala → ...s/adam/projections/FieldEnumeration.scala
diff --git a/...enomics/adam/projections/Projection.scala → ...enomics/adam/projections/Projection.scala b/...enomics/adam/projections/Projection.scala → ...enomics/adam/projections/Projection.scala
diff --git a/...org/bdgenomics/adam/rdd/ADAMContext.scala → ...org/bdgenomics/adam/rdd/ADAMContext.scala b/...org/bdgenomics/adam/rdd/ADAMContext.scala → ...org/bdgenomics/adam/rdd/ADAMContext.scala
diff --git a/...ics/adam/rdd/ADAMParquetInputFormat.scala → ...ics/adam/rdd/ADAMParquetInputFormat.scala b/...ics/adam/rdd/ADAMParquetInputFormat.scala → ...ics/adam/rdd/ADAMParquetInputFormat.scala
diff --git a/...dgenomics/adam/rdd/ADAMRDDFunctions.scala → ...dgenomics/adam/rdd/ADAMRDDFunctions.scala b/...dgenomics/adam/rdd/ADAMRDDFunctions.scala → ...dgenomics/adam/rdd/ADAMRDDFunctions.scala
diff --git a/.../org/bdgenomics/adam/rdd/FileMerger.scala → .../org/bdgenomics/adam/rdd/FileMerger.scala b/.../org/bdgenomics/adam/rdd/FileMerger.scala → .../org/bdgenomics/adam/rdd/FileMerger.scala
diff --git a/.../org/bdgenomics/adam/rdd/GenomeBins.scala → .../org/bdgenomics/adam/rdd/GenomeBins.scala b/.../org/bdgenomics/adam/rdd/GenomeBins.scala → .../org/bdgenomics/adam/rdd/GenomeBins.scala
diff --git a/...s/adam/rdd/GenomicDatasetConversion.scala → ...s/adam/rdd/GenomicDatasetConversion.scala b/...s/adam/rdd/GenomicDatasetConversion.scala → ...s/adam/rdd/GenomicDatasetConversion.scala
diff --git a/...nomics/adam/rdd/GenomicPartitioners.scala → ...nomics/adam/rdd/GenomicPartitioners.scala b/...nomics/adam/rdd/GenomicPartitioners.scala → ...nomics/adam/rdd/GenomicPartitioners.scala
diff --git a/.../org/bdgenomics/adam/rdd/GenomicRDD.scala → .../org/bdgenomics/adam/rdd/GenomicRDD.scala b/.../org/bdgenomics/adam/rdd/GenomicRDD.scala → .../org/bdgenomics/adam/rdd/GenomicRDD.scala
diff --git a/...org/bdgenomics/adam/rdd/InFormatter.scala → ...org/bdgenomics/adam/rdd/InFormatter.scala b/...org/bdgenomics/adam/rdd/InFormatter.scala → ...org/bdgenomics/adam/rdd/InFormatter.scala
diff --git a/...cs/adam/rdd/ManualRegionPartitioner.scala → ...cs/adam/rdd/ManualRegionPartitioner.scala b/...cs/adam/rdd/ManualRegionPartitioner.scala → ...cs/adam/rdd/ManualRegionPartitioner.scala
diff --git a/...rg/bdgenomics/adam/rdd/OutFormatter.scala → ...rg/bdgenomics/adam/rdd/OutFormatter.scala b/...rg/bdgenomics/adam/rdd/OutFormatter.scala → ...rg/bdgenomics/adam/rdd/OutFormatter.scala
diff --git a/...enomics/adam/rdd/ParallelFileMerger.scala → ...enomics/adam/rdd/ParallelFileMerger.scala b/...enomics/adam/rdd/ParallelFileMerger.scala → ...enomics/adam/rdd/ParallelFileMerger.scala
diff --git a/...omics/adam/rdd/ReferencePartitioner.scala → ...omics/adam/rdd/ReferencePartitioner.scala b/...omics/adam/rdd/ReferencePartitioner.scala → ...omics/adam/rdd/ReferencePartitioner.scala
diff --git a/.../org/bdgenomics/adam/rdd/RegionJoin.scala → .../org/bdgenomics/adam/rdd/RegionJoin.scala b/.../org/bdgenomics/adam/rdd/RegionJoin.scala → .../org/bdgenomics/adam/rdd/RegionJoin.scala
diff --git a/...bdgenomics/adam/rdd/SAMHeaderWriter.scala → ...bdgenomics/adam/rdd/SAMHeaderWriter.scala b/...bdgenomics/adam/rdd/SAMHeaderWriter.scala → ...bdgenomics/adam/rdd/SAMHeaderWriter.scala
diff --git a/...genomics/adam/rdd/ShuffleRegionJoin.scala → ...genomics/adam/rdd/ShuffleRegionJoin.scala b/...genomics/adam/rdd/ShuffleRegionJoin.scala → ...genomics/adam/rdd/ShuffleRegionJoin.scala
diff --git a/.../bdgenomics/adam/rdd/TreeRegionJoin.scala → .../bdgenomics/adam/rdd/TreeRegionJoin.scala b/.../bdgenomics/adam/rdd/TreeRegionJoin.scala → .../bdgenomics/adam/rdd/TreeRegionJoin.scala
diff --git a/.../bdgenomics/adam/rdd/VCFHeaderUtils.scala → .../bdgenomics/adam/rdd/VCFHeaderUtils.scala b/.../bdgenomics/adam/rdd/VCFHeaderUtils.scala → .../bdgenomics/adam/rdd/VCFHeaderUtils.scala
diff --git a/.../rdd/contig/FlankReferenceFragments.scala → .../rdd/contig/FlankReferenceFragments.scala b/.../rdd/contig/FlankReferenceFragments.scala → .../rdd/contig/FlankReferenceFragments.scala
diff --git a/.../contig/NucleotideContigFragmentRDD.scala → .../contig/NucleotideContigFragmentRDD.scala b/.../contig/NucleotideContigFragmentRDD.scala → .../contig/NucleotideContigFragmentRDD.scala
diff --git a/...ics/adam/rdd/feature/BEDInFormatter.scala → ...ics/adam/rdd/feature/BEDInFormatter.scala b/...ics/adam/rdd/feature/BEDInFormatter.scala → ...ics/adam/rdd/feature/BEDInFormatter.scala
diff --git a/...cs/adam/rdd/feature/BEDOutFormatter.scala → ...cs/adam/rdd/feature/BEDOutFormatter.scala b/...cs/adam/rdd/feature/BEDOutFormatter.scala → ...cs/adam/rdd/feature/BEDOutFormatter.scala
diff --git a/...nomics/adam/rdd/feature/CoverageRDD.scala → ...nomics/adam/rdd/feature/CoverageRDD.scala b/...nomics/adam/rdd/feature/CoverageRDD.scala → ...nomics/adam/rdd/feature/CoverageRDD.scala
diff --git a/...mics/adam/rdd/feature/FeatureParser.scala → ...mics/adam/rdd/feature/FeatureParser.scala b/...mics/adam/rdd/feature/FeatureParser.scala → ...mics/adam/rdd/feature/FeatureParser.scala
diff --git a/...enomics/adam/rdd/feature/FeatureRDD.scala → ...enomics/adam/rdd/feature/FeatureRDD.scala b/...enomics/adam/rdd/feature/FeatureRDD.scala → ...enomics/adam/rdd/feature/FeatureRDD.scala
diff --git a/...dgenomics/adam/rdd/feature/Features.scala → ...dgenomics/adam/rdd/feature/Features.scala b/...dgenomics/adam/rdd/feature/Features.scala → ...dgenomics/adam/rdd/feature/Features.scala
diff --git a/...s/adam/rdd/feature/GFF3HeaderWriter.scala → ...s/adam/rdd/feature/GFF3HeaderWriter.scala b/...s/adam/rdd/feature/GFF3HeaderWriter.scala → ...s/adam/rdd/feature/GFF3HeaderWriter.scala
diff --git a/...cs/adam/rdd/feature/GFF3InFormatter.scala → ...cs/adam/rdd/feature/GFF3InFormatter.scala b/...cs/adam/rdd/feature/GFF3InFormatter.scala → ...cs/adam/rdd/feature/GFF3InFormatter.scala
diff --git a/...s/adam/rdd/feature/GFF3OutFormatter.scala → ...s/adam/rdd/feature/GFF3OutFormatter.scala b/...s/adam/rdd/feature/GFF3OutFormatter.scala → ...s/adam/rdd/feature/GFF3OutFormatter.scala
diff --git a/...ics/adam/rdd/feature/GTFInFormatter.scala → ...ics/adam/rdd/feature/GTFInFormatter.scala b/...ics/adam/rdd/feature/GTFInFormatter.scala → ...ics/adam/rdd/feature/GTFInFormatter.scala
diff --git a/...cs/adam/rdd/feature/GTFOutFormatter.scala → ...cs/adam/rdd/feature/GTFOutFormatter.scala b/...cs/adam/rdd/feature/GTFOutFormatter.scala → ...cs/adam/rdd/feature/GTFOutFormatter.scala
diff --git a/...m/rdd/feature/NarrowPeakInFormatter.scala → ...m/rdd/feature/NarrowPeakInFormatter.scala b/...m/rdd/feature/NarrowPeakInFormatter.scala → ...m/rdd/feature/NarrowPeakInFormatter.scala
diff --git a/.../rdd/feature/NarrowPeakOutFormatter.scala → .../rdd/feature/NarrowPeakOutFormatter.scala b/.../rdd/feature/NarrowPeakOutFormatter.scala → .../rdd/feature/NarrowPeakOutFormatter.scala
diff --git a/...omics/adam/rdd/fragment/FragmentRDD.scala → ...omics/adam/rdd/fragment/FragmentRDD.scala b/...omics/adam/rdd/fragment/FragmentRDD.scala → ...omics/adam/rdd/fragment/FragmentRDD.scala
diff --git a/...ragment/InterleavedFASTQInFormatter.scala → ...ragment/InterleavedFASTQInFormatter.scala b/...ragment/InterleavedFASTQInFormatter.scala → ...ragment/InterleavedFASTQInFormatter.scala
diff --git a/...s/adam/rdd/fragment/Tab5InFormatter.scala → ...s/adam/rdd/fragment/Tab5InFormatter.scala b/...s/adam/rdd/fragment/Tab5InFormatter.scala → ...s/adam/rdd/fragment/Tab5InFormatter.scala
diff --git a/...s/adam/rdd/fragment/Tab6InFormatter.scala → ...s/adam/rdd/fragment/Tab6InFormatter.scala b/...s/adam/rdd/fragment/Tab6InFormatter.scala → ...s/adam/rdd/fragment/Tab6InFormatter.scala
diff --git a/...s/adam/rdd/read/ADAMBAMOutputFormat.scala → ...s/adam/rdd/read/ADAMBAMOutputFormat.scala b/...s/adam/rdd/read/ADAMBAMOutputFormat.scala → ...s/adam/rdd/read/ADAMBAMOutputFormat.scala
diff --git a/.../adam/rdd/read/ADAMCRAMOutputFormat.scala → .../adam/rdd/read/ADAMCRAMOutputFormat.scala b/.../adam/rdd/read/ADAMCRAMOutputFormat.scala → .../adam/rdd/read/ADAMCRAMOutputFormat.scala
diff --git a/...s/adam/rdd/read/ADAMSAMOutputFormat.scala → ...s/adam/rdd/read/ADAMSAMOutputFormat.scala b/...s/adam/rdd/read/ADAMSAMOutputFormat.scala → ...s/adam/rdd/read/ADAMSAMOutputFormat.scala
diff --git a/...cs/adam/rdd/read/AlignmentRecordRDD.scala → ...cs/adam/rdd/read/AlignmentRecordRDD.scala b/...cs/adam/rdd/read/AlignmentRecordRDD.scala → ...cs/adam/rdd/read/AlignmentRecordRDD.scala
diff --git a/...ics/adam/rdd/read/AnySAMInFormatter.scala → ...ics/adam/rdd/read/AnySAMInFormatter.scala b/...ics/adam/rdd/read/AnySAMInFormatter.scala → ...ics/adam/rdd/read/AnySAMInFormatter.scala
diff --git a/...cs/adam/rdd/read/AnySAMOutFormatter.scala → ...cs/adam/rdd/read/AnySAMOutFormatter.scala b/...cs/adam/rdd/read/AnySAMOutFormatter.scala → ...cs/adam/rdd/read/AnySAMOutFormatter.scala
diff --git a/...nomics/adam/rdd/read/BAMInFormatter.scala → ...nomics/adam/rdd/read/BAMInFormatter.scala b/...nomics/adam/rdd/read/BAMInFormatter.scala → ...nomics/adam/rdd/read/BAMInFormatter.scala
diff --git a/...genomics/adam/rdd/read/BinQualities.scala → ...genomics/adam/rdd/read/BinQualities.scala b/...genomics/adam/rdd/read/BinQualities.scala → ...genomics/adam/rdd/read/BinQualities.scala
diff --git a/...g/bdgenomics/adam/rdd/read/FlagStat.scala → ...g/bdgenomics/adam/rdd/read/FlagStat.scala b/...g/bdgenomics/adam/rdd/read/FlagStat.scala → ...g/bdgenomics/adam/rdd/read/FlagStat.scala
diff --git a/.../bdgenomics/adam/rdd/read/MDTagging.scala → .../bdgenomics/adam/rdd/read/MDTagging.scala b/.../bdgenomics/adam/rdd/read/MDTagging.scala → .../bdgenomics/adam/rdd/read/MDTagging.scala
diff --git a/...nomics/adam/rdd/read/MarkDuplicates.scala → ...nomics/adam/rdd/read/MarkDuplicates.scala b/...nomics/adam/rdd/read/MarkDuplicates.scala → ...nomics/adam/rdd/read/MarkDuplicates.scala
diff --git a/...adam/rdd/read/ReferencePositionPair.scala → ...adam/rdd/read/ReferencePositionPair.scala b/...adam/rdd/read/ReferencePositionPair.scala → ...adam/rdd/read/ReferencePositionPair.scala
diff --git a/...mics/adam/rdd/read/RepairPartitions.scala → ...mics/adam/rdd/read/RepairPartitions.scala b/...mics/adam/rdd/read/RepairPartitions.scala → ...mics/adam/rdd/read/RepairPartitions.scala
diff --git a/...nomics/adam/rdd/read/SAMInFormatter.scala → ...nomics/adam/rdd/read/SAMInFormatter.scala b/...nomics/adam/rdd/read/SAMInFormatter.scala → ...nomics/adam/rdd/read/SAMInFormatter.scala
diff --git a/...mics/adam/rdd/read/SingleReadBucket.scala → ...mics/adam/rdd/read/SingleReadBucket.scala b/...mics/adam/rdd/read/SingleReadBucket.scala → ...mics/adam/rdd/read/SingleReadBucket.scala
diff --git a/.../realignment/IndelRealignmentTarget.scala → .../realignment/IndelRealignmentTarget.scala b/.../realignment/IndelRealignmentTarget.scala → .../realignment/IndelRealignmentTarget.scala
diff --git a/...rdd/read/realignment/ModPartitioner.scala → ...rdd/read/realignment/ModPartitioner.scala b/...rdd/read/realignment/ModPartitioner.scala → ...rdd/read/realignment/ModPartitioner.scala
diff --git a/.../rdd/read/realignment/RealignIndels.scala → .../rdd/read/realignment/RealignIndels.scala b/.../rdd/read/realignment/RealignIndels.scala → .../rdd/read/realignment/RealignIndels.scala
diff --git a/...realignment/RealignmentTargetFinder.scala → ...realignment/RealignmentTargetFinder.scala b/...realignment/RealignmentTargetFinder.scala → ...realignment/RealignmentTargetFinder.scala
diff --git a/...am/rdd/read/recalibration/Aggregate.scala → ...am/rdd/read/recalibration/Aggregate.scala b/...am/rdd/read/recalibration/Aggregate.scala → ...am/rdd/read/recalibration/Aggregate.scala
diff --git a/...alibration/BaseQualityRecalibration.scala → ...alibration/BaseQualityRecalibration.scala b/...alibration/BaseQualityRecalibration.scala → ...alibration/BaseQualityRecalibration.scala
diff --git a/...am/rdd/read/recalibration/Covariate.scala → ...am/rdd/read/recalibration/Covariate.scala b/...am/rdd/read/recalibration/Covariate.scala → ...am/rdd/read/recalibration/Covariate.scala
diff --git a/...rdd/read/recalibration/CovariateKey.scala → ...rdd/read/recalibration/CovariateKey.scala b/...rdd/read/recalibration/CovariateKey.scala → ...rdd/read/recalibration/CovariateKey.scala
diff --git a/...d/read/recalibration/CovariateSpace.scala → ...d/read/recalibration/CovariateSpace.scala b/...d/read/recalibration/CovariateSpace.scala → ...d/read/recalibration/CovariateSpace.scala
diff --git a/...d/read/recalibration/CycleCovariate.scala → ...d/read/recalibration/CycleCovariate.scala b/...d/read/recalibration/CycleCovariate.scala → ...d/read/recalibration/CycleCovariate.scala
diff --git a/...d/read/recalibration/DinucCovariate.scala → ...d/read/recalibration/DinucCovariate.scala b/...d/read/recalibration/DinucCovariate.scala → ...d/read/recalibration/DinucCovariate.scala
diff --git a/.../rdd/read/recalibration/Observation.scala → .../rdd/read/recalibration/Observation.scala b/.../rdd/read/recalibration/Observation.scala → .../rdd/read/recalibration/Observation.scala
diff --git a/...read/recalibration/ObservationTable.scala → ...read/recalibration/ObservationTable.scala b/...read/recalibration/ObservationTable.scala → ...read/recalibration/ObservationTable.scala
diff --git a/...ad/recalibration/RecalibrationTable.scala → ...ad/recalibration/RecalibrationTable.scala b/...ad/recalibration/RecalibrationTable.scala → ...ad/recalibration/RecalibrationTable.scala
diff --git a/...rdd/read/recalibration/Recalibrator.scala → ...rdd/read/recalibration/Recalibrator.scala b/...rdd/read/recalibration/Recalibrator.scala → ...rdd/read/recalibration/Recalibrator.scala
diff --git a/...dam/rdd/variant/ADAMVCFOutputFormat.scala → ...dam/rdd/variant/ADAMVCFOutputFormat.scala b/...dam/rdd/variant/ADAMVCFOutputFormat.scala → ...dam/rdd/variant/ADAMVCFOutputFormat.scala
diff --git a/...nomics/adam/rdd/variant/GenotypeRDD.scala → ...nomics/adam/rdd/variant/GenotypeRDD.scala b/...nomics/adam/rdd/variant/GenotypeRDD.scala → ...nomics/adam/rdd/variant/GenotypeRDD.scala
diff --git a/...ics/adam/rdd/variant/VCFInFormatter.scala → ...ics/adam/rdd/variant/VCFInFormatter.scala b/...ics/adam/rdd/variant/VCFInFormatter.scala → ...ics/adam/rdd/variant/VCFInFormatter.scala
diff --git a/...cs/adam/rdd/variant/VCFOutFormatter.scala → ...cs/adam/rdd/variant/VCFOutFormatter.scala b/...cs/adam/rdd/variant/VCFOutFormatter.scala → ...cs/adam/rdd/variant/VCFOutFormatter.scala
diff --git a/.../adam/rdd/variant/VariantContextRDD.scala → .../adam/rdd/variant/VariantContextRDD.scala b/.../adam/rdd/variant/VariantContextRDD.scala → .../adam/rdd/variant/VariantContextRDD.scala
diff --git a/...enomics/adam/rdd/variant/VariantRDD.scala → ...enomics/adam/rdd/variant/VariantRDD.scala b/...enomics/adam/rdd/variant/VariantRDD.scala → ...enomics/adam/rdd/variant/VariantRDD.scala
diff --git a/...omics/adam/rich/RichAlignmentRecord.scala → ...omics/adam/rich/RichAlignmentRecord.scala b/...omics/adam/rich/RichAlignmentRecord.scala → ...omics/adam/rich/RichAlignmentRecord.scala
diff --git a/.../org/bdgenomics/adam/rich/RichCigar.scala → .../org/bdgenomics/adam/rich/RichCigar.scala b/.../org/bdgenomics/adam/rich/RichCigar.scala → .../org/bdgenomics/adam/rich/RichCigar.scala
diff --git a/...rg/bdgenomics/adam/rich/RichVariant.scala → ...rg/bdgenomics/adam/rich/RichVariant.scala b/...rg/bdgenomics/adam/rich/RichVariant.scala → ...rg/bdgenomics/adam/rich/RichVariant.scala
diff --git a/...m/serialization/ADAMKryoRegistrator.scala → ...m/serialization/ADAMKryoRegistrator.scala b/...m/serialization/ADAMKryoRegistrator.scala → ...m/serialization/ADAMKryoRegistrator.scala
diff --git a/...bdgenomics/adam/util/AttributeUtils.scala → ...bdgenomics/adam/util/AttributeUtils.scala b/...bdgenomics/adam/util/AttributeUtils.scala → ...bdgenomics/adam/util/AttributeUtils.scala
diff --git a/...bdgenomics/adam/util/FileExtensions.scala → ...bdgenomics/adam/util/FileExtensions.scala b/...bdgenomics/adam/util/FileExtensions.scala → ...bdgenomics/adam/util/FileExtensions.scala
diff --git a/...genomics/adam/util/GenomeFileReader.scala → ...genomics/adam/util/GenomeFileReader.scala b/...genomics/adam/util/GenomeFileReader.scala → ...genomics/adam/util/GenomeFileReader.scala
diff --git a/...genomics/adam/util/IndexedFastaFile.scala → ...genomics/adam/util/IndexedFastaFile.scala b/...genomics/adam/util/IndexedFastaFile.scala → ...genomics/adam/util/IndexedFastaFile.scala
diff --git a/...cs/adam/util/ParquetFileTraversable.scala → ...cs/adam/util/ParquetFileTraversable.scala b/...cs/adam/util/ParquetFileTraversable.scala → ...cs/adam/util/ParquetFileTraversable.scala
diff --git a/.../bdgenomics/adam/util/ParquetLogger.scala → .../bdgenomics/adam/util/ParquetLogger.scala b/.../bdgenomics/adam/util/ParquetLogger.scala → .../bdgenomics/adam/util/ParquetLogger.scala
diff --git a/...org/bdgenomics/adam/util/PhredUtils.scala → ...org/bdgenomics/adam/util/PhredUtils.scala b/...org/bdgenomics/adam/util/PhredUtils.scala → ...org/bdgenomics/adam/util/PhredUtils.scala
diff --git a/...nomics/adam/util/ReferenceContigMap.scala → ...nomics/adam/util/ReferenceContigMap.scala b/...nomics/adam/util/ReferenceContigMap.scala → ...nomics/adam/util/ReferenceContigMap.scala
diff --git a/.../bdgenomics/adam/util/ReferenceFile.scala → .../bdgenomics/adam/util/ReferenceFile.scala b/.../bdgenomics/adam/util/ReferenceFile.scala → .../bdgenomics/adam/util/ReferenceFile.scala
diff --git a/.../adam/util/SequenceDictionaryReader.scala → .../adam/util/SequenceDictionaryReader.scala b/.../adam/util/SequenceDictionaryReader.scala → .../adam/util/SequenceDictionaryReader.scala
diff --git a/...org/bdgenomics/adam/util/TwoBitFile.scala → ...org/bdgenomics/adam/util/TwoBitFile.scala b/...org/bdgenomics/adam/util/TwoBitFile.scala → ...org/bdgenomics/adam/util/TwoBitFile.scala
diff --git a/.../test/resources/HLA_DQB1_05_01_01_02.dict → .../test/resources/HLA_DQB1_05_01_01_02.dict b/.../test/resources/HLA_DQB1_05_01_01_02.dict → .../test/resources/HLA_DQB1_05_01_01_02.dict
diff --git a/...rc/test/resources/HLA_DQB1_05_01_01_02.fa → ...rc/test/resources/HLA_DQB1_05_01_01_02.fa b/...rc/test/resources/HLA_DQB1_05_01_01_02.fa → ...rc/test/resources/HLA_DQB1_05_01_01_02.fa
diff --git a/...est/resources/HLA_DQB1_05_01_01_02.fa.fai → ...est/resources/HLA_DQB1_05_01_01_02.fa.fai b/...est/resources/HLA_DQB1_05_01_01_02.fa.fai → ...est/resources/HLA_DQB1_05_01_01_02.fa.fai
diff --git a/...ources/Homo_sapiens.GRCh37.75.trun100.gtf → ...ources/Homo_sapiens.GRCh37.75.trun100.gtf b/...ources/Homo_sapiens.GRCh37.75.trun100.gtf → ...ources/Homo_sapiens.GRCh37.75.trun100.gtf
diff --git a/...sources/Homo_sapiens.GRCh37.75.trun20.gtf → ...sources/Homo_sapiens.GRCh37.75.trun20.gtf b/...sources/Homo_sapiens.GRCh37.75.trun20.gtf → ...sources/Homo_sapiens.GRCh37.75.trun20.gtf
diff --git a/...st/resources/Hs_Ensembl_example_genes.gtf → ...st/resources/Hs_Ensembl_example_genes.gtf b/...st/resources/Hs_Ensembl_example_genes.gtf → ...st/resources/Hs_Ensembl_example_genes.gtf
diff --git a/...est/resources/NA12878.1_854950_855150.sam → ...est/resources/NA12878.1_854950_855150.sam b/...est/resources/NA12878.1_854950_855150.sam → ...est/resources/NA12878.1_854950_855150.sam
diff --git a/...t/resources/NA12878.1_922305.G_GC_hom.sam → ...t/resources/NA12878.1_922305.G_GC_hom.sam b/...t/resources/NA12878.1_922305.G_GC_hom.sam → ...t/resources/NA12878.1_922305.G_GC_hom.sam
diff --git a/...esources/NA12878.chr22.tiny.freebayes.vcf → ...esources/NA12878.chr22.tiny.freebayes.vcf b/...esources/NA12878.chr22.tiny.freebayes.vcf → ...esources/NA12878.chr22.tiny.freebayes.vcf
diff --git a/adam-core/src/test/resources/NA12878.sam → core/src/test/resources/NA12878.sam b/adam-core/src/test/resources/NA12878.sam → core/src/test/resources/NA12878.sam
diff --git a/...ces/SeqCap_EZ_Exome_v3.hg19.interval_list → ...ces/SeqCap_EZ_Exome_v3.hg19.interval_list b/...ces/SeqCap_EZ_Exome_v3.hg19.interval_list → ...ces/SeqCap_EZ_Exome_v3.hg19.interval_list
diff --git a/.../src/test/resources/artificial.README.txt → .../src/test/resources/artificial.README.txt b/.../src/test/resources/artificial.README.txt → .../src/test/resources/artificial.README.txt
diff --git a/adam-core/src/test/resources/artificial.cram → core/src/test/resources/artificial.cram b/adam-core/src/test/resources/artificial.cram → core/src/test/resources/artificial.cram
diff --git a/adam-core/src/test/resources/artificial.fa → core/src/test/resources/artificial.fa b/adam-core/src/test/resources/artificial.fa → core/src/test/resources/artificial.fa
diff --git a/...core/src/test/resources/artificial.fa.fai → core/src/test/resources/artificial.fa.fai b/...core/src/test/resources/artificial.fa.fai → core/src/test/resources/artificial.fa.fai
diff --git a/...c/test/resources/artificial.realigned.sam → ...c/test/resources/artificial.realigned.sam b/...c/test/resources/artificial.realigned.sam → ...c/test/resources/artificial.realigned.sam
diff --git a/adam-core/src/test/resources/artificial.sam → core/src/test/resources/artificial.sam b/adam-core/src/test/resources/artificial.sam → core/src/test/resources/artificial.sam
diff --git a/adam-core/src/test/resources/badheader.sam → core/src/test/resources/badheader.sam b/adam-core/src/test/resources/badheader.sam → core/src/test/resources/badheader.sam
diff --git a/adam-core/src/test/resources/bqsr1-r1.fq → core/src/test/resources/bqsr1-r1.fq b/adam-core/src/test/resources/bqsr1-r1.fq → core/src/test/resources/bqsr1-r1.fq
diff --git a/adam-core/src/test/resources/bqsr1-r2.fq → core/src/test/resources/bqsr1-r2.fq b/adam-core/src/test/resources/bqsr1-r2.fq → core/src/test/resources/bqsr1-r2.fq
diff --git a/...ore/src/test/resources/bqsr1-ref.observed → core/src/test/resources/bqsr1-ref.observed b/...ore/src/test/resources/bqsr1-ref.observed → core/src/test/resources/bqsr1-ref.observed
diff --git a/adam-core/src/test/resources/bqsr1.sam → core/src/test/resources/bqsr1.sam b/adam-core/src/test/resources/bqsr1.sam → core/src/test/resources/bqsr1.sam
diff --git a/adam-core/src/test/resources/bqsr1.snps → core/src/test/resources/bqsr1.snps b/adam-core/src/test/resources/bqsr1.snps → core/src/test/resources/bqsr1.snps
diff --git a/adam-core/src/test/resources/bqsr1.vcf → core/src/test/resources/bqsr1.vcf b/adam-core/src/test/resources/bqsr1.vcf → core/src/test/resources/bqsr1.vcf
diff --git a/adam-core/src/test/resources/bqsr1.vcf.tbi → core/src/test/resources/bqsr1.vcf.tbi b/adam-core/src/test/resources/bqsr1.vcf.tbi → core/src/test/resources/bqsr1.vcf.tbi
diff --git a/...-core/src/test/resources/chr20.250k.fa.gz → core/src/test/resources/chr20.250k.fa.gz b/...-core/src/test/resources/chr20.250k.fa.gz → core/src/test/resources/chr20.250k.fa.gz
diff --git a/adam-core/src/test/resources/chromInfo.txt → core/src/test/resources/chromInfo.txt b/adam-core/src/test/resources/chromInfo.txt → core/src/test/resources/chromInfo.txt
diff --git a/...c/test/resources/dict_with_accession.dict → ...c/test/resources/dict_with_accession.dict b/...c/test/resources/dict_with_accession.dict → ...c/test/resources/dict_with_accession.dict
diff --git a/adam-core/src/test/resources/dvl1.200.bed → core/src/test/resources/dvl1.200.bed b/adam-core/src/test/resources/dvl1.200.bed → core/src/test/resources/dvl1.200.bed
diff --git a/adam-core/src/test/resources/dvl1.200.gff3 → core/src/test/resources/dvl1.200.gff3 b/adam-core/src/test/resources/dvl1.200.gff3 → core/src/test/resources/dvl1.200.gff3
diff --git a/adam-core/src/test/resources/dvl1.200.gtf → core/src/test/resources/dvl1.200.gtf b/adam-core/src/test/resources/dvl1.200.gtf → core/src/test/resources/dvl1.200.gtf
diff --git a/...re/src/test/resources/env_test_command.sh → core/src/test/resources/env_test_command.sh b/...re/src/test/resources/env_test_command.sh → core/src/test/resources/env_test_command.sh
diff --git a/...src/test/resources/example_intervals.list → ...src/test/resources/example_intervals.list b/...src/test/resources/example_intervals.list → ...src/test/resources/example_intervals.list
diff --git a/adam-core/src/test/resources/fastq_noqual.fq → core/src/test/resources/fastq_noqual.fq b/adam-core/src/test/resources/fastq_noqual.fq → core/src/test/resources/fastq_noqual.fq
diff --git a/...-core/src/test/resources/fastq_sample1.fq → core/src/test/resources/fastq_sample1.fq b/...-core/src/test/resources/fastq_sample1.fq → core/src/test/resources/fastq_sample1.fq
diff --git a/...e/src/test/resources/fastq_sample1.fq.bgz → core/src/test/resources/fastq_sample1.fq.bgz b/...e/src/test/resources/fastq_sample1.fq.bgz → core/src/test/resources/fastq_sample1.fq.bgz
diff --git a/...e/src/test/resources/fastq_sample1.fq.bz2 → core/src/test/resources/fastq_sample1.fq.bz2 b/...e/src/test/resources/fastq_sample1.fq.bz2 → core/src/test/resources/fastq_sample1.fq.bz2
diff --git a/...re/src/test/resources/fastq_sample1.fq.gz → core/src/test/resources/fastq_sample1.fq.gz b/...re/src/test/resources/fastq_sample1.fq.gz → core/src/test/resources/fastq_sample1.fq.gz
diff --git a/...-core/src/test/resources/fastq_sample2.fq → core/src/test/resources/fastq_sample2.fq b/...-core/src/test/resources/fastq_sample2.fq → core/src/test/resources/fastq_sample2.fq
diff --git a/...-core/src/test/resources/fastq_sample3.fq → core/src/test/resources/fastq_sample3.fq b/...-core/src/test/resources/fastq_sample3.fq → core/src/test/resources/fastq_sample3.fq
diff --git a/...-core/src/test/resources/fastq_sample4.fq → core/src/test/resources/fastq_sample4.fq b/...-core/src/test/resources/fastq_sample4.fq → core/src/test/resources/fastq_sample4.fq
diff --git a/...-core/src/test/resources/fastq_to_usam.py → core/src/test/resources/fastq_to_usam.py b/...-core/src/test/resources/fastq_to_usam.py → core/src/test/resources/fastq_to_usam.py
diff --git a/...gencode.chr20.transcript_names.head10.txt → ...gencode.chr20.transcript_names.head10.txt b/...gencode.chr20.transcript_names.head10.txt → ...gencode.chr20.transcript_names.head10.txt
diff --git a/...ces/gencode.v19.annotation.chr20.250k.gtf → ...ces/gencode.v19.annotation.chr20.250k.gtf b/...ces/gencode.v19.annotation.chr20.250k.gtf → ...ces/gencode.v19.annotation.chr20.250k.gtf
diff --git a/...ces/gencode.v19.pc_transcripts.250k.fa.gz → ...ces/gencode.v19.pc_transcripts.250k.fa.gz b/...ces/gencode.v19.pc_transcripts.250k.fa.gz → ...ces/gencode.v19.pc_transcripts.250k.fa.gz
diff --git a/...sources/gencode.v7.annotation.trunc10.bed → ...sources/gencode.v7.annotation.trunc10.bed b/...sources/gencode.v7.annotation.trunc10.bed → ...sources/gencode.v7.annotation.trunc10.bed
diff --git a/...esources/gvcf_dir/gvcf_multiallelic.g.vcf → ...esources/gvcf_dir/gvcf_multiallelic.g.vcf b/...esources/gvcf_dir/gvcf_multiallelic.g.vcf → ...esources/gvcf_dir/gvcf_multiallelic.g.vcf
diff --git a/...es/gvcf_dir/gvcf_multiallelic_noPLs.g.vcf → ...es/gvcf_dir/gvcf_multiallelic_noPLs.g.vcf b/...es/gvcf_dir/gvcf_multiallelic_noPLs.g.vcf → ...es/gvcf_dir/gvcf_multiallelic_noPLs.g.vcf
diff --git a/...ources/gvcf_multiallelic/multiallelic.vcf → ...ources/gvcf_multiallelic/multiallelic.vcf b/...ources/gvcf_multiallelic/multiallelic.vcf → ...ources/gvcf_multiallelic/multiallelic.vcf
diff --git a/adam-core/src/test/resources/hg19.chrM.2bit → core/src/test/resources/hg19.chrM.2bit b/adam-core/src/test/resources/hg19.chrM.2bit → core/src/test/resources/hg19.chrM.2bit
diff --git a/adam-core/src/test/resources/hg19.genome → core/src/test/resources/hg19.genome b/adam-core/src/test/resources/hg19.genome → core/src/test/resources/hg19.genome
diff --git a/adam-core/src/test/resources/hg19.genome.txt → core/src/test/resources/hg19.genome.txt b/adam-core/src/test/resources/hg19.genome.txt → core/src/test/resources/hg19.genome.txt
diff --git a/adam-core/src/test/resources/hs37d5.dict → core/src/test/resources/hs37d5.dict b/adam-core/src/test/resources/hs37d5.dict → core/src/test/resources/hs37d5.dict
diff --git a/...core/src/test/resources/hs38DH_chr1_10.fa → core/src/test/resources/hs38DH_chr1_10.fa b/...core/src/test/resources/hs38DH_chr1_10.fa → core/src/test/resources/hs38DH_chr1_10.fa
diff --git a/...st/resources/human_g1k_v37_chr1_59kb.2bit → ...st/resources/human_g1k_v37_chr1_59kb.2bit b/...st/resources/human_g1k_v37_chr1_59kb.2bit → ...st/resources/human_g1k_v37_chr1_59kb.2bit
diff --git a/...t/resources/human_g1k_v37_chr1_59kb.fasta → ...t/resources/human_g1k_v37_chr1_59kb.fasta b/...t/resources/human_g1k_v37_chr1_59kb.fasta → ...t/resources/human_g1k_v37_chr1_59kb.fasta
diff --git a/...re/src/test/resources/improper_pairs_1.fq → core/src/test/resources/improper_pairs_1.fq b/...re/src/test/resources/improper_pairs_1.fq → core/src/test/resources/improper_pairs_1.fq
diff --git a/...re/src/test/resources/improper_pairs_2.fq → core/src/test/resources/improper_pairs_2.fq b/...re/src/test/resources/improper_pairs_2.fq → core/src/test/resources/improper_pairs_2.fq
diff --git a/.../test/resources/indexed_bams/sorted.2.bam → .../test/resources/indexed_bams/sorted.2.bam b/.../test/resources/indexed_bams/sorted.2.bam → .../test/resources/indexed_bams/sorted.2.bam
diff --git a/...t/resources/indexed_bams/sorted.2.bam.bai → ...t/resources/indexed_bams/sorted.2.bam.bai b/...t/resources/indexed_bams/sorted.2.bam.bai → ...t/resources/indexed_bams/sorted.2.bam.bai
diff --git a/...rc/test/resources/indexed_bams/sorted.bam → ...rc/test/resources/indexed_bams/sorted.bam b/...rc/test/resources/indexed_bams/sorted.bam → ...rc/test/resources/indexed_bams/sorted.bam
diff --git a/...est/resources/indexed_bams/sorted.bam.bai → ...est/resources/indexed_bams/sorted.bam.bai b/...est/resources/indexed_bams/sorted.bam.bai → ...est/resources/indexed_bams/sorted.bam.bai
diff --git a/...t/resources/interleaved_fastq_sample1.ifq → ...t/resources/interleaved_fastq_sample1.ifq b/...t/resources/interleaved_fastq_sample1.ifq → ...t/resources/interleaved_fastq_sample1.ifq
diff --git a/...sources/interleaved_fastq_sample1.ifq.bgz → ...sources/interleaved_fastq_sample1.ifq.bgz b/...sources/interleaved_fastq_sample1.ifq.bgz → ...sources/interleaved_fastq_sample1.ifq.bgz
diff --git a/...sources/interleaved_fastq_sample1.ifq.bz2 → ...sources/interleaved_fastq_sample1.ifq.bz2 b/...sources/interleaved_fastq_sample1.ifq.bz2 → ...sources/interleaved_fastq_sample1.ifq.bz2
diff --git a/...esources/interleaved_fastq_sample1.ifq.gz → ...esources/interleaved_fastq_sample1.ifq.gz b/...esources/interleaved_fastq_sample1.ifq.gz → ...esources/interleaved_fastq_sample1.ifq.gz
diff --git a/...rces/interleaved_fastq_sample1.ifq.output → ...rces/interleaved_fastq_sample1.ifq.output b/...rces/interleaved_fastq_sample1.ifq.output → ...rces/interleaved_fastq_sample1.ifq.output
diff --git a/...t/resources/interleaved_fastq_sample2.ifq → ...t/resources/interleaved_fastq_sample2.ifq b/...t/resources/interleaved_fastq_sample2.ifq → ...t/resources/interleaved_fastq_sample2.ifq
diff --git a/...rces/interleaved_fastq_sample2.ifq.output → ...rces/interleaved_fastq_sample2.ifq.output b/...rces/interleaved_fastq_sample2.ifq.output → ...rces/interleaved_fastq_sample2.ifq.output
diff --git a/...t/resources/interleaved_fastq_sample3.ifq → ...t/resources/interleaved_fastq_sample3.ifq b/...t/resources/interleaved_fastq_sample3.ifq → ...t/resources/interleaved_fastq_sample3.ifq
diff --git a/...rces/interleaved_fastq_sample3.ifq.output → ...rces/interleaved_fastq_sample3.ifq.output b/...rces/interleaved_fastq_sample3.ifq.output → ...rces/interleaved_fastq_sample3.ifq.output
diff --git a/...t/resources/interleaved_fastq_sample4.ifq → ...t/resources/interleaved_fastq_sample4.ifq b/...t/resources/interleaved_fastq_sample4.ifq → ...t/resources/interleaved_fastq_sample4.ifq
diff --git a/...rces/interleaved_fastq_sample4.ifq.output → ...rces/interleaved_fastq_sample4.ifq.output b/...rces/interleaved_fastq_sample4.ifq.output → ...rces/interleaved_fastq_sample4.ifq.output
diff --git a/...t/resources/interleaved_fastq_sample5.ifq → ...t/resources/interleaved_fastq_sample5.ifq b/...t/resources/interleaved_fastq_sample5.ifq → ...t/resources/interleaved_fastq_sample5.ifq
diff --git a/...rces/interleaved_fastq_sample5.ifq.output → ...rces/interleaved_fastq_sample5.ifq.output b/...rces/interleaved_fastq_sample5.ifq.output → ...rces/interleaved_fastq_sample5.ifq.output
diff --git a/...-core/src/test/resources/log4j.properties → core/src/test/resources/log4j.properties b/...-core/src/test/resources/log4j.properties → core/src/test/resources/log4j.properties
diff --git a/...ore/src/test/resources/multiline_fastq.fq → core/src/test/resources/multiline_fastq.fq b/...ore/src/test/resources/multiline_fastq.fq → core/src/test/resources/multiline_fastq.fq
diff --git a/adam-core/src/test/resources/ordered.sam → core/src/test/resources/ordered.sam b/adam-core/src/test/resources/ordered.sam → core/src/test/resources/ordered.sam
diff --git a/...core/src/test/resources/proper_pairs_1.fq → core/src/test/resources/proper_pairs_1.fq b/...core/src/test/resources/proper_pairs_1.fq → core/src/test/resources/proper_pairs_1.fq
diff --git a/...core/src/test/resources/proper_pairs_2.fq → core/src/test/resources/proper_pairs_2.fq b/...core/src/test/resources/proper_pairs_2.fq → core/src/test/resources/proper_pairs_2.fq
diff --git a/adam-core/src/test/resources/queryname.sam → core/src/test/resources/queryname.sam b/adam-core/src/test/resources/queryname.sam → core/src/test/resources/queryname.sam
diff --git a/adam-core/src/test/resources/random.vcf → core/src/test/resources/random.vcf b/adam-core/src/test/resources/random.vcf → core/src/test/resources/random.vcf
diff --git a/adam-core/src/test/resources/reads-0-2-0 → core/src/test/resources/reads-0-2-0 b/adam-core/src/test/resources/reads-0-2-0 → core/src/test/resources/reads-0-2-0
diff --git a/adam-core/src/test/resources/reads12.sam → core/src/test/resources/reads12.sam b/adam-core/src/test/resources/reads12.sam → core/src/test/resources/reads12.sam
diff --git a/...core/src/test/resources/reads12_diff1.sam → core/src/test/resources/reads12_diff1.sam b/...core/src/test/resources/reads12_diff1.sam → core/src/test/resources/reads12_diff1.sam
diff --git a/adam-core/src/test/resources/reads13.sam → core/src/test/resources/reads13.sam b/adam-core/src/test/resources/reads13.sam → core/src/test/resources/reads13.sam
diff --git a/adam-core/src/test/resources/reads21.sam → core/src/test/resources/reads21.sam b/adam-core/src/test/resources/reads21.sam → core/src/test/resources/reads21.sam
diff --git a/...core/src/test/resources/sample1.query.sam → core/src/test/resources/sample1.query.sam b/...core/src/test/resources/sample1.query.sam → core/src/test/resources/sample1.query.sam
diff --git a/.../src/test/resources/sample1.queryname.sam → .../src/test/resources/sample1.queryname.sam b/.../src/test/resources/sample1.queryname.sam → .../src/test/resources/sample1.queryname.sam
diff --git a/...re/src/test/resources/sample_coverage.bed → core/src/test/resources/sample_coverage.bed b/...re/src/test/resources/sample_coverage.bed → core/src/test/resources/sample_coverage.bed
diff --git a/.../resources/single_fastq_sample1.fq.output → .../resources/single_fastq_sample1.fq.output b/.../resources/single_fastq_sample1.fq.output → .../resources/single_fastq_sample1.fq.output
diff --git a/.../resources/single_fastq_sample2.fq.output → .../resources/single_fastq_sample2.fq.output b/.../resources/single_fastq_sample2.fq.output → .../resources/single_fastq_sample2.fq.output
diff --git a/.../resources/single_fastq_sample3.fq.output → .../resources/single_fastq_sample3.fq.output b/.../resources/single_fastq_sample3.fq.output → .../resources/single_fastq_sample3.fq.output
diff --git a/.../resources/single_fastq_sample4.fq.output → .../resources/single_fastq_sample4.fq.output b/.../resources/single_fastq_sample4.fq.output → .../resources/single_fastq_sample4.fq.output
diff --git a/adam-core/src/test/resources/small.1.bed → core/src/test/resources/small.1.bed b/adam-core/src/test/resources/small.1.bed → core/src/test/resources/small.1.bed
diff --git a/...ore/src/test/resources/small.1.narrowPeak → core/src/test/resources/small.1.narrowPeak b/...ore/src/test/resources/small.1.narrowPeak → core/src/test/resources/small.1.narrowPeak
diff --git a/adam-core/src/test/resources/small.1.sam → core/src/test/resources/small.1.sam b/adam-core/src/test/resources/small.1.sam → core/src/test/resources/small.1.sam
diff --git a/adam-core/src/test/resources/small.1_12.bed → core/src/test/resources/small.1_12.bed b/adam-core/src/test/resources/small.1_12.bed → core/src/test/resources/small.1_12.bed
diff --git a/adam-core/src/test/resources/small.sam → core/src/test/resources/small.sam b/adam-core/src/test/resources/small.sam → core/src/test/resources/small.sam