moved all files into new gradle structure

this is to prepare for changing the build system from ant to gradle moving the sources and test data into a more standard gradle project structure src/java -> src/main/java src/c -> src/main/c src/tests -> src/test/java src/tests/resources -> src/test/resources testdata -> src/test/resources src/scripts -> scripts it's important to maintain this as a seperate commit to keep git's rename tracking working correctly
samtools · May 13, 2016 · 909381a · 909381a
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diff --git a/src/scripts/build_intel_deflater.sh → scripts/build_intel_deflater.sh b/src/scripts/build_intel_deflater.sh → scripts/build_intel_deflater.sh
diff --git a/src/scripts/explain_sam_flags.py → scripts/explain_sam_flags.py b/src/scripts/explain_sam_flags.py → scripts/explain_sam_flags.py
diff --git a/src/scripts/release_picard.sh → scripts/release_picard.sh b/src/scripts/release_picard.sh → scripts/release_picard.sh
diff --git a/src/c/inteldeflater/IntelDeflater.c → src/main/c/inteldeflater/IntelDeflater.c b/src/c/inteldeflater/IntelDeflater.c → src/main/c/inteldeflater/IntelDeflater.c
diff --git a/src/c/inteldeflater/README → src/main/c/inteldeflater/README b/src/c/inteldeflater/README → src/main/c/inteldeflater/README
diff --git a/src/c/inteldeflater/igzip_lib.h → src/main/c/inteldeflater/igzip_lib.h b/src/c/inteldeflater/igzip_lib.h → src/main/c/inteldeflater/igzip_lib.h
diff --git a/src/c/inteldeflater/internal_state_size.h → ...ain/c/inteldeflater/internal_state_size.h b/src/c/inteldeflater/internal_state_size.h → ...ain/c/inteldeflater/internal_state_size.h
diff --git a/src/c/inteldeflater/types.h → src/main/c/inteldeflater/types.h b/src/c/inteldeflater/types.h → src/main/c/inteldeflater/types.h
diff --git a/...htsjdk/samtools/AbstractBAMFileIndex.java → ...htsjdk/samtools/AbstractBAMFileIndex.java b/...htsjdk/samtools/AbstractBAMFileIndex.java → ...htsjdk/samtools/AbstractBAMFileIndex.java
diff --git a/...jdk/samtools/AbstractSAMHeaderRecord.java → ...jdk/samtools/AbstractSAMHeaderRecord.java b/...jdk/samtools/AbstractSAMHeaderRecord.java → ...jdk/samtools/AbstractSAMHeaderRecord.java
diff --git a/src/java/htsjdk/samtools/AlignmentBlock.java → .../java/htsjdk/samtools/AlignmentBlock.java b/src/java/htsjdk/samtools/AlignmentBlock.java → .../java/htsjdk/samtools/AlignmentBlock.java
diff --git a/...a/htsjdk/samtools/AsyncSAMFileWriter.java → ...a/htsjdk/samtools/AsyncSAMFileWriter.java b/...a/htsjdk/samtools/AsyncSAMFileWriter.java → ...a/htsjdk/samtools/AsyncSAMFileWriter.java
diff --git a/...ava/htsjdk/samtools/BAMFileConstants.java → ...ava/htsjdk/samtools/BAMFileConstants.java b/...ava/htsjdk/samtools/BAMFileConstants.java → ...ava/htsjdk/samtools/BAMFileConstants.java
diff --git a/src/java/htsjdk/samtools/BAMFileReader.java → ...n/java/htsjdk/samtools/BAMFileReader.java b/src/java/htsjdk/samtools/BAMFileReader.java → ...n/java/htsjdk/samtools/BAMFileReader.java
diff --git a/src/java/htsjdk/samtools/BAMFileSpan.java → ...ain/java/htsjdk/samtools/BAMFileSpan.java b/src/java/htsjdk/samtools/BAMFileSpan.java → ...ain/java/htsjdk/samtools/BAMFileSpan.java
diff --git a/src/java/htsjdk/samtools/BAMFileWriter.java → ...n/java/htsjdk/samtools/BAMFileWriter.java b/src/java/htsjdk/samtools/BAMFileWriter.java → ...n/java/htsjdk/samtools/BAMFileWriter.java
diff --git a/src/java/htsjdk/samtools/BAMIndex.java → src/main/java/htsjdk/samtools/BAMIndex.java b/src/java/htsjdk/samtools/BAMIndex.java → src/main/java/htsjdk/samtools/BAMIndex.java
diff --git a/...java/htsjdk/samtools/BAMIndexContent.java → ...java/htsjdk/samtools/BAMIndexContent.java b/...java/htsjdk/samtools/BAMIndexContent.java → ...java/htsjdk/samtools/BAMIndexContent.java
diff --git a/...ava/htsjdk/samtools/BAMIndexMetaData.java → ...ava/htsjdk/samtools/BAMIndexMetaData.java b/...ava/htsjdk/samtools/BAMIndexMetaData.java → ...ava/htsjdk/samtools/BAMIndexMetaData.java
diff --git a/src/java/htsjdk/samtools/BAMIndexWriter.java → .../java/htsjdk/samtools/BAMIndexWriter.java b/src/java/htsjdk/samtools/BAMIndexWriter.java → .../java/htsjdk/samtools/BAMIndexWriter.java
diff --git a/src/java/htsjdk/samtools/BAMIndexer.java → ...main/java/htsjdk/samtools/BAMIndexer.java b/src/java/htsjdk/samtools/BAMIndexer.java → ...main/java/htsjdk/samtools/BAMIndexer.java
diff --git a/src/java/htsjdk/samtools/BAMRecord.java → src/main/java/htsjdk/samtools/BAMRecord.java b/src/java/htsjdk/samtools/BAMRecord.java → src/main/java/htsjdk/samtools/BAMRecord.java
diff --git a/src/java/htsjdk/samtools/BAMRecordCodec.java → .../java/htsjdk/samtools/BAMRecordCodec.java b/src/java/htsjdk/samtools/BAMRecordCodec.java → .../java/htsjdk/samtools/BAMRecordCodec.java
diff --git a/src/java/htsjdk/samtools/BamFileIoUtils.java → .../java/htsjdk/samtools/BamFileIoUtils.java b/src/java/htsjdk/samtools/BamFileIoUtils.java → .../java/htsjdk/samtools/BamFileIoUtils.java
diff --git a/...va/htsjdk/samtools/BamIndexValidator.java → ...va/htsjdk/samtools/BamIndexValidator.java b/...va/htsjdk/samtools/BamIndexValidator.java → ...va/htsjdk/samtools/BamIndexValidator.java
diff --git a/src/java/htsjdk/samtools/Bin.java → src/main/java/htsjdk/samtools/Bin.java b/src/java/htsjdk/samtools/Bin.java → src/main/java/htsjdk/samtools/Bin.java
diff --git a/src/java/htsjdk/samtools/BinList.java → src/main/java/htsjdk/samtools/BinList.java b/src/java/htsjdk/samtools/BinList.java → src/main/java/htsjdk/samtools/BinList.java
diff --git a/...htsjdk/samtools/BinaryBAMIndexWriter.java → ...htsjdk/samtools/BinaryBAMIndexWriter.java b/...htsjdk/samtools/BinaryBAMIndexWriter.java → ...htsjdk/samtools/BinaryBAMIndexWriter.java
diff --git a/...ava/htsjdk/samtools/BinaryCigarCodec.java → ...ava/htsjdk/samtools/BinaryCigarCodec.java b/...ava/htsjdk/samtools/BinaryCigarCodec.java → ...ava/htsjdk/samtools/BinaryCigarCodec.java
diff --git a/src/java/htsjdk/samtools/BinaryTagCodec.java → .../java/htsjdk/samtools/BinaryTagCodec.java b/src/java/htsjdk/samtools/BinaryTagCodec.java → .../java/htsjdk/samtools/BinaryTagCodec.java
diff --git a/.../htsjdk/samtools/BinningIndexBuilder.java → .../htsjdk/samtools/BinningIndexBuilder.java b/.../htsjdk/samtools/BinningIndexBuilder.java → .../htsjdk/samtools/BinningIndexBuilder.java
diff --git a/.../htsjdk/samtools/BinningIndexContent.java → .../htsjdk/samtools/BinningIndexContent.java b/.../htsjdk/samtools/BinningIndexContent.java → .../htsjdk/samtools/BinningIndexContent.java
diff --git a/...a/htsjdk/samtools/BrowseableBAMIndex.java → ...a/htsjdk/samtools/BrowseableBAMIndex.java b/...a/htsjdk/samtools/BrowseableBAMIndex.java → ...a/htsjdk/samtools/BrowseableBAMIndex.java
diff --git a/src/java/htsjdk/samtools/CRAMBAIIndexer.java → .../java/htsjdk/samtools/CRAMBAIIndexer.java b/src/java/htsjdk/samtools/CRAMBAIIndexer.java → .../java/htsjdk/samtools/CRAMBAIIndexer.java
diff --git a/...k/samtools/CRAMContainerStreamWriter.java → ...k/samtools/CRAMContainerStreamWriter.java b/...k/samtools/CRAMContainerStreamWriter.java → ...k/samtools/CRAMContainerStreamWriter.java
diff --git a/src/java/htsjdk/samtools/CRAMFileReader.java → .../java/htsjdk/samtools/CRAMFileReader.java b/src/java/htsjdk/samtools/CRAMFileReader.java → .../java/htsjdk/samtools/CRAMFileReader.java
diff --git a/src/java/htsjdk/samtools/CRAMFileWriter.java → .../java/htsjdk/samtools/CRAMFileWriter.java b/src/java/htsjdk/samtools/CRAMFileWriter.java → .../java/htsjdk/samtools/CRAMFileWriter.java
diff --git a/src/java/htsjdk/samtools/CRAMIterator.java → ...in/java/htsjdk/samtools/CRAMIterator.java b/src/java/htsjdk/samtools/CRAMIterator.java → ...in/java/htsjdk/samtools/CRAMIterator.java
diff --git a/.../htsjdk/samtools/CachingBAMFileIndex.java → .../htsjdk/samtools/CachingBAMFileIndex.java b/.../htsjdk/samtools/CachingBAMFileIndex.java → .../htsjdk/samtools/CachingBAMFileIndex.java
diff --git a/...samtools/ChainedDownsamplingIterator.java → ...samtools/ChainedDownsamplingIterator.java b/...samtools/ChainedDownsamplingIterator.java → ...samtools/ChainedDownsamplingIterator.java
diff --git a/src/java/htsjdk/samtools/Chunk.java → src/main/java/htsjdk/samtools/Chunk.java b/src/java/htsjdk/samtools/Chunk.java → src/main/java/htsjdk/samtools/Chunk.java
diff --git a/src/java/htsjdk/samtools/Cigar.java → src/main/java/htsjdk/samtools/Cigar.java b/src/java/htsjdk/samtools/Cigar.java → src/main/java/htsjdk/samtools/Cigar.java
diff --git a/src/java/htsjdk/samtools/CigarElement.java → ...in/java/htsjdk/samtools/CigarElement.java b/src/java/htsjdk/samtools/CigarElement.java → ...in/java/htsjdk/samtools/CigarElement.java
diff --git a/src/java/htsjdk/samtools/CigarOperator.java → ...n/java/htsjdk/samtools/CigarOperator.java b/src/java/htsjdk/samtools/CigarOperator.java → ...n/java/htsjdk/samtools/CigarOperator.java
diff --git a/...samtools/ComparableSamRecordIterator.java → ...samtools/ComparableSamRecordIterator.java b/...samtools/ComparableSamRecordIterator.java → ...samtools/ComparableSamRecordIterator.java
diff --git a/...s/ConstantMemoryDownsamplingIterator.java → ...s/ConstantMemoryDownsamplingIterator.java b/...s/ConstantMemoryDownsamplingIterator.java → ...s/ConstantMemoryDownsamplingIterator.java
diff --git a/...samtools/CoordinateSortedPairInfoMap.java → ...samtools/CoordinateSortedPairInfoMap.java b/...samtools/CoordinateSortedPairInfoMap.java → ...samtools/CoordinateSortedPairInfoMap.java
diff --git a/.../htsjdk/samtools/CustomReaderFactory.java → .../htsjdk/samtools/CustomReaderFactory.java b/.../htsjdk/samtools/CustomReaderFactory.java → .../htsjdk/samtools/CustomReaderFactory.java
diff --git a/...jdk/samtools/DefaultSAMRecordFactory.java → ...jdk/samtools/DefaultSAMRecordFactory.java b/...jdk/samtools/DefaultSAMRecordFactory.java → ...jdk/samtools/DefaultSAMRecordFactory.java
diff --git a/src/java/htsjdk/samtools/Defaults.java → src/main/java/htsjdk/samtools/Defaults.java b/src/java/htsjdk/samtools/Defaults.java → src/main/java/htsjdk/samtools/Defaults.java
diff --git a/...tsjdk/samtools/DiskBasedBAMFileIndex.java → ...tsjdk/samtools/DiskBasedBAMFileIndex.java b/...tsjdk/samtools/DiskBasedBAMFileIndex.java → ...tsjdk/samtools/DiskBasedBAMFileIndex.java
diff --git a/...htsjdk/samtools/DownsamplingIterator.java → ...htsjdk/samtools/DownsamplingIterator.java b/...htsjdk/samtools/DownsamplingIterator.java → ...htsjdk/samtools/DownsamplingIterator.java
diff --git a/...samtools/DownsamplingIteratorFactory.java → ...samtools/DownsamplingIteratorFactory.java b/...samtools/DownsamplingIteratorFactory.java → ...samtools/DownsamplingIteratorFactory.java
diff --git a/...dk/samtools/DuplicateScoringStrategy.java → ...dk/samtools/DuplicateScoringStrategy.java b/...dk/samtools/DuplicateScoringStrategy.java → ...dk/samtools/DuplicateScoringStrategy.java
diff --git a/src/java/htsjdk/samtools/DuplicateSet.java → ...in/java/htsjdk/samtools/DuplicateSet.java b/src/java/htsjdk/samtools/DuplicateSet.java → ...in/java/htsjdk/samtools/DuplicateSet.java
diff --git a/...htsjdk/samtools/DuplicateSetIterator.java → ...htsjdk/samtools/DuplicateSetIterator.java b/...htsjdk/samtools/DuplicateSetIterator.java → ...htsjdk/samtools/DuplicateSetIterator.java
diff --git a/...sjdk/samtools/FileTruncatedException.java → ...sjdk/samtools/FileTruncatedException.java b/...sjdk/samtools/FileTruncatedException.java → ...sjdk/samtools/FileTruncatedException.java
diff --git a/src/java/htsjdk/samtools/FixBAMFile.java → ...main/java/htsjdk/samtools/FixBAMFile.java b/src/java/htsjdk/samtools/FixBAMFile.java → ...main/java/htsjdk/samtools/FixBAMFile.java
diff --git a/...ava/htsjdk/samtools/GenomicIndexUtil.java → ...ava/htsjdk/samtools/GenomicIndexUtil.java b/...ava/htsjdk/samtools/GenomicIndexUtil.java → ...ava/htsjdk/samtools/GenomicIndexUtil.java
diff --git a/...ols/HighAccuracyDownsamplingIterator.java → ...ols/HighAccuracyDownsamplingIterator.java b/...ols/HighAccuracyDownsamplingIterator.java → ...ols/HighAccuracyDownsamplingIterator.java
diff --git a/src/java/htsjdk/samtools/LinearIndex.java → ...ain/java/htsjdk/samtools/LinearIndex.java b/src/java/htsjdk/samtools/LinearIndex.java → ...ain/java/htsjdk/samtools/LinearIndex.java
diff --git a/...dk/samtools/MergingSamRecordIterator.java → ...dk/samtools/MergingSamRecordIterator.java b/...dk/samtools/MergingSamRecordIterator.java → ...dk/samtools/MergingSamRecordIterator.java
diff --git a/.../samtools/NotPrimarySkippingIterator.java → .../samtools/NotPrimarySkippingIterator.java b/.../samtools/NotPrimarySkippingIterator.java → .../samtools/NotPrimarySkippingIterator.java
diff --git a/src/java/htsjdk/samtools/QueryInterval.java → ...n/java/htsjdk/samtools/QueryInterval.java b/src/java/htsjdk/samtools/QueryInterval.java → ...n/java/htsjdk/samtools/QueryInterval.java
diff --git a/...htsjdk/samtools/ReservedTagConstants.java → ...htsjdk/samtools/ReservedTagConstants.java b/...htsjdk/samtools/ReservedTagConstants.java → ...htsjdk/samtools/ReservedTagConstants.java
diff --git a/...ls/SAMBinaryTagAndUnsignedArrayValue.java → ...ls/SAMBinaryTagAndUnsignedArrayValue.java b/...ls/SAMBinaryTagAndUnsignedArrayValue.java → ...ls/SAMBinaryTagAndUnsignedArrayValue.java
diff --git a/...htsjdk/samtools/SAMBinaryTagAndValue.java → ...htsjdk/samtools/SAMBinaryTagAndValue.java b/...htsjdk/samtools/SAMBinaryTagAndValue.java → ...htsjdk/samtools/SAMBinaryTagAndValue.java
diff --git a/src/java/htsjdk/samtools/SAMException.java → ...in/java/htsjdk/samtools/SAMException.java b/src/java/htsjdk/samtools/SAMException.java → ...in/java/htsjdk/samtools/SAMException.java
diff --git a/src/java/htsjdk/samtools/SAMFileHeader.java → ...n/java/htsjdk/samtools/SAMFileHeader.java b/src/java/htsjdk/samtools/SAMFileHeader.java → ...n/java/htsjdk/samtools/SAMFileHeader.java
diff --git a/src/java/htsjdk/samtools/SAMFileReader.java → ...n/java/htsjdk/samtools/SAMFileReader.java b/src/java/htsjdk/samtools/SAMFileReader.java → ...n/java/htsjdk/samtools/SAMFileReader.java
diff --git a/src/java/htsjdk/samtools/SAMFileSource.java → ...n/java/htsjdk/samtools/SAMFileSource.java b/src/java/htsjdk/samtools/SAMFileSource.java → ...n/java/htsjdk/samtools/SAMFileSource.java
diff --git a/src/java/htsjdk/samtools/SAMFileSpan.java → ...ain/java/htsjdk/samtools/SAMFileSpan.java b/src/java/htsjdk/samtools/SAMFileSpan.java → ...ain/java/htsjdk/samtools/SAMFileSpan.java
diff --git a/...sjdk/samtools/SAMFileTruncatedReader.java → ...sjdk/samtools/SAMFileTruncatedReader.java b/...sjdk/samtools/SAMFileTruncatedReader.java → ...sjdk/samtools/SAMFileTruncatedReader.java
diff --git a/src/java/htsjdk/samtools/SAMFileWriter.java → ...n/java/htsjdk/samtools/SAMFileWriter.java b/src/java/htsjdk/samtools/SAMFileWriter.java → ...n/java/htsjdk/samtools/SAMFileWriter.java
diff --git a/...htsjdk/samtools/SAMFileWriterFactory.java → ...htsjdk/samtools/SAMFileWriterFactory.java b/...htsjdk/samtools/SAMFileWriterFactory.java → ...htsjdk/samtools/SAMFileWriterFactory.java
diff --git a/...va/htsjdk/samtools/SAMFileWriterImpl.java → ...va/htsjdk/samtools/SAMFileWriterImpl.java b/...va/htsjdk/samtools/SAMFileWriterImpl.java → ...va/htsjdk/samtools/SAMFileWriterImpl.java
diff --git a/src/java/htsjdk/samtools/SAMFlag.java → src/main/java/htsjdk/samtools/SAMFlag.java b/src/java/htsjdk/samtools/SAMFlag.java → src/main/java/htsjdk/samtools/SAMFlag.java
diff --git a/...a/htsjdk/samtools/SAMFormatException.java → ...a/htsjdk/samtools/SAMFormatException.java b/...a/htsjdk/samtools/SAMFormatException.java → ...a/htsjdk/samtools/SAMFormatException.java
diff --git a/...k/samtools/SAMHeaderRecordComparator.java → ...k/samtools/SAMHeaderRecordComparator.java b/...k/samtools/SAMHeaderRecordComparator.java → ...k/samtools/SAMHeaderRecordComparator.java
diff --git a/src/java/htsjdk/samtools/SAMLineParser.java → ...n/java/htsjdk/samtools/SAMLineParser.java b/src/java/htsjdk/samtools/SAMLineParser.java → ...n/java/htsjdk/samtools/SAMLineParser.java
diff --git a/...ava/htsjdk/samtools/SAMProgramRecord.java → ...ava/htsjdk/samtools/SAMProgramRecord.java b/...ava/htsjdk/samtools/SAMProgramRecord.java → ...ava/htsjdk/samtools/SAMProgramRecord.java
diff --git a/...a/htsjdk/samtools/SAMReadGroupRecord.java → ...a/htsjdk/samtools/SAMReadGroupRecord.java b/...a/htsjdk/samtools/SAMReadGroupRecord.java → ...a/htsjdk/samtools/SAMReadGroupRecord.java
diff --git a/src/java/htsjdk/samtools/SAMRecord.java → src/main/java/htsjdk/samtools/SAMRecord.java b/src/java/htsjdk/samtools/SAMRecord.java → src/main/java/htsjdk/samtools/SAMRecord.java
diff --git a/.../htsjdk/samtools/SAMRecordComparator.java → .../htsjdk/samtools/SAMRecordComparator.java b/.../htsjdk/samtools/SAMRecordComparator.java → .../htsjdk/samtools/SAMRecordComparator.java
diff --git a/...mtools/SAMRecordCoordinateComparator.java → ...mtools/SAMRecordCoordinateComparator.java b/...mtools/SAMRecordCoordinateComparator.java → ...mtools/SAMRecordCoordinateComparator.java
diff --git a/...amtools/SAMRecordDuplicateComparator.java → ...amtools/SAMRecordDuplicateComparator.java b/...amtools/SAMRecordDuplicateComparator.java → ...amtools/SAMRecordDuplicateComparator.java
diff --git a/...ava/htsjdk/samtools/SAMRecordFactory.java → ...ava/htsjdk/samtools/SAMRecordFactory.java b/...ava/htsjdk/samtools/SAMRecordFactory.java → ...ava/htsjdk/samtools/SAMRecordFactory.java
diff --git a/...va/htsjdk/samtools/SAMRecordIterator.java → ...va/htsjdk/samtools/SAMRecordIterator.java b/...va/htsjdk/samtools/SAMRecordIterator.java → ...va/htsjdk/samtools/SAMRecordIterator.java
diff --git a/...amtools/SAMRecordQueryHashComparator.java → ...amtools/SAMRecordQueryHashComparator.java b/...amtools/SAMRecordQueryHashComparator.java → ...amtools/SAMRecordQueryHashComparator.java
diff --git a/...amtools/SAMRecordQueryNameComparator.java → ...amtools/SAMRecordQueryNameComparator.java b/...amtools/SAMRecordQueryNameComparator.java → ...amtools/SAMRecordQueryNameComparator.java
diff --git a/.../htsjdk/samtools/SAMRecordSetBuilder.java → .../htsjdk/samtools/SAMRecordSetBuilder.java b/.../htsjdk/samtools/SAMRecordSetBuilder.java → .../htsjdk/samtools/SAMRecordSetBuilder.java
diff --git a/src/java/htsjdk/samtools/SAMRecordUtil.java → ...n/java/htsjdk/samtools/SAMRecordUtil.java b/src/java/htsjdk/samtools/SAMRecordUtil.java → ...n/java/htsjdk/samtools/SAMRecordUtil.java
diff --git a/...tsjdk/samtools/SAMSequenceDictionary.java → ...tsjdk/samtools/SAMSequenceDictionary.java b/...tsjdk/samtools/SAMSequenceDictionary.java → ...tsjdk/samtools/SAMSequenceDictionary.java
diff --git a/...va/htsjdk/samtools/SAMSequenceRecord.java → ...va/htsjdk/samtools/SAMSequenceRecord.java b/...va/htsjdk/samtools/SAMSequenceRecord.java → ...va/htsjdk/samtools/SAMSequenceRecord.java
diff --git a/.../htsjdk/samtools/SAMSortOrderChecker.java → .../htsjdk/samtools/SAMSortOrderChecker.java b/.../htsjdk/samtools/SAMSortOrderChecker.java → .../htsjdk/samtools/SAMSortOrderChecker.java
diff --git a/src/java/htsjdk/samtools/SAMTag.java → src/main/java/htsjdk/samtools/SAMTag.java b/src/java/htsjdk/samtools/SAMTag.java → src/main/java/htsjdk/samtools/SAMTag.java
diff --git a/src/java/htsjdk/samtools/SAMTagUtil.java → ...main/java/htsjdk/samtools/SAMTagUtil.java b/src/java/htsjdk/samtools/SAMTagUtil.java → ...main/java/htsjdk/samtools/SAMTagUtil.java
diff --git a/src/java/htsjdk/samtools/SAMTestUtil.java → ...ain/java/htsjdk/samtools/SAMTestUtil.java b/src/java/htsjdk/samtools/SAMTestUtil.java → ...ain/java/htsjdk/samtools/SAMTestUtil.java
diff --git a/...a/htsjdk/samtools/SAMTextHeaderCodec.java → ...a/htsjdk/samtools/SAMTextHeaderCodec.java b/...a/htsjdk/samtools/SAMTextHeaderCodec.java → ...a/htsjdk/samtools/SAMTextHeaderCodec.java
diff --git a/src/java/htsjdk/samtools/SAMTextReader.java → ...n/java/htsjdk/samtools/SAMTextReader.java b/src/java/htsjdk/samtools/SAMTextReader.java → ...n/java/htsjdk/samtools/SAMTextReader.java
diff --git a/src/java/htsjdk/samtools/SAMTextWriter.java → ...n/java/htsjdk/samtools/SAMTextWriter.java b/src/java/htsjdk/samtools/SAMTextWriter.java → ...n/java/htsjdk/samtools/SAMTextWriter.java
diff --git a/src/java/htsjdk/samtools/SAMTools.java → src/main/java/htsjdk/samtools/SAMTools.java b/src/java/htsjdk/samtools/SAMTools.java → src/main/java/htsjdk/samtools/SAMTools.java
diff --git a/src/java/htsjdk/samtools/SAMUtils.java → src/main/java/htsjdk/samtools/SAMUtils.java b/src/java/htsjdk/samtools/SAMUtils.java → src/main/java/htsjdk/samtools/SAMUtils.java
diff --git a/...a/htsjdk/samtools/SAMValidationError.java → ...a/htsjdk/samtools/SAMValidationError.java b/...a/htsjdk/samtools/SAMValidationError.java → ...a/htsjdk/samtools/SAMValidationError.java
diff --git a/src/java/htsjdk/samtools/SQTagUtil.java → src/main/java/htsjdk/samtools/SQTagUtil.java b/src/java/htsjdk/samtools/SQTagUtil.java → src/main/java/htsjdk/samtools/SQTagUtil.java
diff --git a/src/java/htsjdk/samtools/SRAFileReader.java → ...n/java/htsjdk/samtools/SRAFileReader.java b/src/java/htsjdk/samtools/SRAFileReader.java → ...n/java/htsjdk/samtools/SRAFileReader.java
diff --git a/src/java/htsjdk/samtools/SRAIndex.java → src/main/java/htsjdk/samtools/SRAIndex.java b/src/java/htsjdk/samtools/SRAIndex.java → src/main/java/htsjdk/samtools/SRAIndex.java
diff --git a/src/java/htsjdk/samtools/SRAIterator.java → ...ain/java/htsjdk/samtools/SRAIterator.java b/src/java/htsjdk/samtools/SRAIterator.java → ...ain/java/htsjdk/samtools/SRAIterator.java
diff --git a/.../htsjdk/samtools/SamFileHeaderMerger.java → .../htsjdk/samtools/SamFileHeaderMerger.java b/.../htsjdk/samtools/SamFileHeaderMerger.java → .../htsjdk/samtools/SamFileHeaderMerger.java
diff --git a/...ava/htsjdk/samtools/SamFileValidator.java → ...ava/htsjdk/samtools/SamFileValidator.java b/...ava/htsjdk/samtools/SamFileValidator.java → ...ava/htsjdk/samtools/SamFileValidator.java
diff --git a/src/java/htsjdk/samtools/SamFiles.java → src/main/java/htsjdk/samtools/SamFiles.java b/src/java/htsjdk/samtools/SamFiles.java → src/main/java/htsjdk/samtools/SamFiles.java
diff --git a/src/java/htsjdk/samtools/SamIndexes.java → ...main/java/htsjdk/samtools/SamIndexes.java b/src/java/htsjdk/samtools/SamIndexes.java → ...main/java/htsjdk/samtools/SamIndexes.java
diff --git a/...ava/htsjdk/samtools/SamInputResource.java → ...ava/htsjdk/samtools/SamInputResource.java b/...ava/htsjdk/samtools/SamInputResource.java → ...ava/htsjdk/samtools/SamInputResource.java
diff --git a/src/java/htsjdk/samtools/SamPairUtil.java → ...ain/java/htsjdk/samtools/SamPairUtil.java b/src/java/htsjdk/samtools/SamPairUtil.java → ...ain/java/htsjdk/samtools/SamPairUtil.java
diff --git a/src/java/htsjdk/samtools/SamReader.java → src/main/java/htsjdk/samtools/SamReader.java b/src/java/htsjdk/samtools/SamReader.java → src/main/java/htsjdk/samtools/SamReader.java
diff --git a/...ava/htsjdk/samtools/SamReaderFactory.java → ...ava/htsjdk/samtools/SamReaderFactory.java b/...ava/htsjdk/samtools/SamReaderFactory.java → ...ava/htsjdk/samtools/SamReaderFactory.java
diff --git a/src/java/htsjdk/samtools/SamStreams.java → ...main/java/htsjdk/samtools/SamStreams.java b/src/java/htsjdk/samtools/SamStreams.java → ...main/java/htsjdk/samtools/SamStreams.java
diff --git a/...ndaryOrSupplementarySkippingIterator.java → ...ndaryOrSupplementarySkippingIterator.java b/...ndaryOrSupplementarySkippingIterator.java → ...ndaryOrSupplementarySkippingIterator.java
diff --git a/.../StreamInflatingIndexingOutputStream.java → .../StreamInflatingIndexingOutputStream.java b/.../StreamInflatingIndexingOutputStream.java → .../StreamInflatingIndexingOutputStream.java
diff --git a/...amtools/TagValueAndUnsignedArrayFlag.java → ...amtools/TagValueAndUnsignedArrayFlag.java b/...amtools/TagValueAndUnsignedArrayFlag.java → ...amtools/TagValueAndUnsignedArrayFlag.java
diff --git a/src/java/htsjdk/samtools/TextCigarCodec.java → .../java/htsjdk/samtools/TextCigarCodec.java b/src/java/htsjdk/samtools/TextCigarCodec.java → .../java/htsjdk/samtools/TextCigarCodec.java
diff --git a/src/java/htsjdk/samtools/TextTagCodec.java → ...in/java/htsjdk/samtools/TextTagCodec.java b/src/java/htsjdk/samtools/TextTagCodec.java → ...in/java/htsjdk/samtools/TextTagCodec.java
diff --git a/...tsjdk/samtools/TextualBAMIndexWriter.java → ...tsjdk/samtools/TextualBAMIndexWriter.java b/...tsjdk/samtools/TextualBAMIndexWriter.java → ...tsjdk/samtools/TextualBAMIndexWriter.java
diff --git a/...htsjdk/samtools/ValidationStringency.java → ...htsjdk/samtools/ValidationStringency.java b/...htsjdk/samtools/ValidationStringency.java → ...htsjdk/samtools/ValidationStringency.java
diff --git a/...ava/htsjdk/samtools/apps/TimeChannel.java → ...ava/htsjdk/samtools/apps/TimeChannel.java b/...ava/htsjdk/samtools/apps/TimeChannel.java → ...ava/htsjdk/samtools/apps/TimeChannel.java
diff --git a/...k/samtools/apps/TimeRandomAccessFile.java → ...k/samtools/apps/TimeRandomAccessFile.java b/...k/samtools/apps/TimeRandomAccessFile.java → ...k/samtools/apps/TimeRandomAccessFile.java
diff --git a/src/java/htsjdk/samtools/cram/CRAIEntry.java → .../java/htsjdk/samtools/cram/CRAIEntry.java b/src/java/htsjdk/samtools/cram/CRAIEntry.java → .../java/htsjdk/samtools/cram/CRAIEntry.java
diff --git a/src/java/htsjdk/samtools/cram/CRAIIndex.java → .../java/htsjdk/samtools/cram/CRAIIndex.java b/src/java/htsjdk/samtools/cram/CRAIIndex.java → .../java/htsjdk/samtools/cram/CRAIIndex.java
diff --git a/...a/htsjdk/samtools/cram/CRAMException.java → ...a/htsjdk/samtools/cram/CRAMException.java b/...a/htsjdk/samtools/cram/CRAMException.java → ...a/htsjdk/samtools/cram/CRAMException.java
diff --git a/.../cram/build/CompressionHeaderFactory.java → .../cram/build/CompressionHeaderFactory.java b/.../cram/build/CompressionHeaderFactory.java → .../cram/build/CompressionHeaderFactory.java
diff --git a/...samtools/cram/build/ContainerFactory.java → ...samtools/cram/build/ContainerFactory.java b/...samtools/cram/build/ContainerFactory.java → ...samtools/cram/build/ContainerFactory.java
diff --git a/.../samtools/cram/build/ContainerParser.java → .../samtools/cram/build/ContainerParser.java b/.../samtools/cram/build/ContainerParser.java → .../samtools/cram/build/ContainerParser.java
diff --git a/...ols/cram/build/Cram2SamRecordFactory.java → ...ols/cram/build/Cram2SamRecordFactory.java b/...ols/cram/build/Cram2SamRecordFactory.java → ...ols/cram/build/Cram2SamRecordFactory.java
diff --git a/...ols/cram/build/CramContainerIterator.java → ...ols/cram/build/CramContainerIterator.java b/...ols/cram/build/CramContainerIterator.java → ...ols/cram/build/CramContainerIterator.java
diff --git a/...va/htsjdk/samtools/cram/build/CramIO.java → ...va/htsjdk/samtools/cram/build/CramIO.java b/...va/htsjdk/samtools/cram/build/CramIO.java → ...va/htsjdk/samtools/cram/build/CramIO.java
diff --git a/...k/samtools/cram/build/CramNormalizer.java → ...k/samtools/cram/build/CramNormalizer.java b/...k/samtools/cram/build/CramNormalizer.java → ...k/samtools/cram/build/CramNormalizer.java
diff --git a/...cram/build/CramSpanContainerIterator.java → ...cram/build/CramSpanContainerIterator.java b/...cram/build/CramSpanContainerIterator.java → ...cram/build/CramSpanContainerIterator.java
diff --git a/...ols/cram/build/Sam2CramRecordFactory.java → ...ols/cram/build/Sam2CramRecordFactory.java b/...ols/cram/build/Sam2CramRecordFactory.java → ...ols/cram/build/Sam2CramRecordFactory.java
diff --git a/...ava/htsjdk/samtools/cram/build/Utils.java → ...ava/htsjdk/samtools/cram/build/Utils.java b/...ava/htsjdk/samtools/cram/build/Utils.java → ...ava/htsjdk/samtools/cram/build/Utils.java
diff --git a/...ools/cram/common/CramVersionPolicies.java → ...ools/cram/common/CramVersionPolicies.java b/...ools/cram/common/CramVersionPolicies.java → ...ools/cram/common/CramVersionPolicies.java
diff --git a/...dk/samtools/cram/common/CramVersions.java → ...dk/samtools/cram/common/CramVersions.java b/...dk/samtools/cram/common/CramVersions.java → ...dk/samtools/cram/common/CramVersions.java
diff --git a/...sjdk/samtools/cram/common/IntHashMap.java → ...sjdk/samtools/cram/common/IntHashMap.java b/...sjdk/samtools/cram/common/IntHashMap.java → ...sjdk/samtools/cram/common/IntHashMap.java
diff --git a/...sjdk/samtools/cram/common/MutableInt.java → ...sjdk/samtools/cram/common/MutableInt.java b/...sjdk/samtools/cram/common/MutableInt.java → ...sjdk/samtools/cram/common/MutableInt.java
diff --git a/.../htsjdk/samtools/cram/common/Version.java → .../htsjdk/samtools/cram/common/Version.java b/.../htsjdk/samtools/cram/common/Version.java → .../htsjdk/samtools/cram/common/Version.java
diff --git a/...ols/cram/digest/AbstractSerialDigest.java → ...ols/cram/digest/AbstractSerialDigest.java b/...ols/cram/digest/AbstractSerialDigest.java → ...ols/cram/digest/AbstractSerialDigest.java
diff --git a/.../samtools/cram/digest/ByteSumCombine.java → .../samtools/cram/digest/ByteSumCombine.java b/.../samtools/cram/digest/ByteSumCombine.java → .../samtools/cram/digest/ByteSumCombine.java
diff --git a/.../htsjdk/samtools/cram/digest/Combine.java → .../htsjdk/samtools/cram/digest/Combine.java b/.../htsjdk/samtools/cram/digest/Combine.java → .../htsjdk/samtools/cram/digest/Combine.java
diff --git a/.../samtools/cram/digest/ContentDigests.java → .../samtools/cram/digest/ContentDigests.java b/.../samtools/cram/digest/ContentDigests.java → .../samtools/cram/digest/ContentDigests.java
diff --git a/...jdk/samtools/cram/digest/Crc32Hasher.java → ...jdk/samtools/cram/digest/Crc32Hasher.java b/...jdk/samtools/cram/digest/Crc32Hasher.java → ...jdk/samtools/cram/digest/Crc32Hasher.java
diff --git a/...mtools/cram/digest/IntegerSumCombine.java → ...mtools/cram/digest/IntegerSumCombine.java b/...mtools/cram/digest/IntegerSumCombine.java → ...mtools/cram/digest/IntegerSumCombine.java
diff --git a/...ools/cram/digest/MessageDigestHasher.java → ...ools/cram/digest/MessageDigestHasher.java b/...ools/cram/digest/MessageDigestHasher.java → ...ools/cram/digest/MessageDigestHasher.java
diff --git a/...a/htsjdk/samtools/cram/digest/SERIES.java → ...a/htsjdk/samtools/cram/digest/SERIES.java b/...a/htsjdk/samtools/cram/digest/SERIES.java → ...a/htsjdk/samtools/cram/digest/SERIES.java
diff --git a/...tools/cram/encoding/AbstractBitCodec.java → ...tools/cram/encoding/AbstractBitCodec.java b/...tools/cram/encoding/AbstractBitCodec.java → ...tools/cram/encoding/AbstractBitCodec.java
diff --git a/...tools/cram/encoding/BetaIntegerCodec.java → ...tools/cram/encoding/BetaIntegerCodec.java b/...tools/cram/encoding/BetaIntegerCodec.java → ...tools/cram/encoding/BetaIntegerCodec.java
diff --git a/...ls/cram/encoding/BetaIntegerEncoding.java → ...ls/cram/encoding/BetaIntegerEncoding.java b/...ls/cram/encoding/BetaIntegerEncoding.java → ...ls/cram/encoding/BetaIntegerEncoding.java
diff --git a/...sjdk/samtools/cram/encoding/BitCodec.java → ...sjdk/samtools/cram/encoding/BitCodec.java b/...sjdk/samtools/cram/encoding/BitCodec.java → ...sjdk/samtools/cram/encoding/BitCodec.java
diff --git a/...s/cram/encoding/ByteArrayLenEncoding.java → ...s/cram/encoding/ByteArrayLenEncoding.java b/...s/cram/encoding/ByteArrayLenEncoding.java → ...s/cram/encoding/ByteArrayLenEncoding.java
diff --git a/.../cram/encoding/ByteArrayStopEncoding.java → .../cram/encoding/ByteArrayStopEncoding.java b/.../cram/encoding/ByteArrayStopEncoding.java → .../cram/encoding/ByteArrayStopEncoding.java
diff --git a/...dk/samtools/cram/encoding/DataSeries.java → ...dk/samtools/cram/encoding/DataSeries.java b/...dk/samtools/cram/encoding/DataSeries.java → ...dk/samtools/cram/encoding/DataSeries.java
diff --git a/...samtools/cram/encoding/DataSeriesMap.java → ...samtools/cram/encoding/DataSeriesMap.java b/...samtools/cram/encoding/DataSeriesMap.java → ...samtools/cram/encoding/DataSeriesMap.java
diff --git a/...amtools/cram/encoding/DataSeriesType.java → ...amtools/cram/encoding/DataSeriesType.java b/...amtools/cram/encoding/DataSeriesType.java → ...amtools/cram/encoding/DataSeriesType.java
diff --git a/...sjdk/samtools/cram/encoding/Encoding.java → ...sjdk/samtools/cram/encoding/Encoding.java b/...sjdk/samtools/cram/encoding/Encoding.java → ...sjdk/samtools/cram/encoding/Encoding.java
diff --git a/...mtools/cram/encoding/EncodingFactory.java → ...mtools/cram/encoding/EncodingFactory.java b/...mtools/cram/encoding/EncodingFactory.java → ...mtools/cram/encoding/EncodingFactory.java
diff --git a/...cram/encoding/ExternalByteArrayCodec.java → ...cram/encoding/ExternalByteArrayCodec.java b/...cram/encoding/ExternalByteArrayCodec.java → ...cram/encoding/ExternalByteArrayCodec.java
diff --git a/...m/encoding/ExternalByteArrayEncoding.java → ...m/encoding/ExternalByteArrayEncoding.java b/...m/encoding/ExternalByteArrayEncoding.java → ...m/encoding/ExternalByteArrayEncoding.java
diff --git a/...ools/cram/encoding/ExternalByteCodec.java → ...ools/cram/encoding/ExternalByteCodec.java b/...ools/cram/encoding/ExternalByteCodec.java → ...ools/cram/encoding/ExternalByteCodec.java
diff --git a/...s/cram/encoding/ExternalByteEncoding.java → ...s/cram/encoding/ExternalByteEncoding.java b/...s/cram/encoding/ExternalByteEncoding.java → ...s/cram/encoding/ExternalByteEncoding.java
diff --git a/...ols/cram/encoding/ExternalCompressor.java → ...ols/cram/encoding/ExternalCompressor.java b/...ols/cram/encoding/ExternalCompressor.java → ...ols/cram/encoding/ExternalCompressor.java
diff --git a/...s/cram/encoding/ExternalIntegerCodec.java → ...s/cram/encoding/ExternalIntegerCodec.java b/...s/cram/encoding/ExternalIntegerCodec.java → ...s/cram/encoding/ExternalIntegerCodec.java
diff --git a/...ram/encoding/ExternalIntegerEncoding.java → ...ram/encoding/ExternalIntegerEncoding.java b/...ram/encoding/ExternalIntegerEncoding.java → ...ram/encoding/ExternalIntegerEncoding.java
diff --git a/...ools/cram/encoding/ExternalLongCodec.java → ...ools/cram/encoding/ExternalLongCodec.java b/...ools/cram/encoding/ExternalLongCodec.java → ...ools/cram/encoding/ExternalLongCodec.java
diff --git a/...s/cram/encoding/ExternalLongEncoding.java → ...s/cram/encoding/ExternalLongEncoding.java b/...s/cram/encoding/ExternalLongEncoding.java → ...s/cram/encoding/ExternalLongEncoding.java
diff --git a/...ools/cram/encoding/GammaIntegerCodec.java → ...ools/cram/encoding/GammaIntegerCodec.java b/...ools/cram/encoding/GammaIntegerCodec.java → ...ools/cram/encoding/GammaIntegerCodec.java
diff --git a/...s/cram/encoding/GammaIntegerEncoding.java → ...s/cram/encoding/GammaIntegerEncoding.java b/...s/cram/encoding/GammaIntegerEncoding.java → ...s/cram/encoding/GammaIntegerEncoding.java
diff --git a/...ols/cram/encoding/GolombIntegerCodec.java → ...ols/cram/encoding/GolombIntegerCodec.java b/...ols/cram/encoding/GolombIntegerCodec.java → ...ols/cram/encoding/GolombIntegerCodec.java
diff --git a/.../cram/encoding/GolombIntegerEncoding.java → .../cram/encoding/GolombIntegerEncoding.java b/.../cram/encoding/GolombIntegerEncoding.java → .../cram/encoding/GolombIntegerEncoding.java
diff --git a/...mtools/cram/encoding/GolombLongCodec.java → ...mtools/cram/encoding/GolombLongCodec.java b/...mtools/cram/encoding/GolombLongCodec.java → ...mtools/cram/encoding/GolombLongCodec.java
diff --git a/...ols/cram/encoding/GolombLongEncoding.java → ...ols/cram/encoding/GolombLongEncoding.java b/...ols/cram/encoding/GolombLongEncoding.java → ...ols/cram/encoding/GolombLongEncoding.java
diff --git a/...cram/encoding/GolombRiceIntegerCodec.java → ...cram/encoding/GolombRiceIntegerCodec.java b/...cram/encoding/GolombRiceIntegerCodec.java → ...cram/encoding/GolombRiceIntegerCodec.java
diff --git a/...m/encoding/GolombRiceIntegerEncoding.java → ...m/encoding/GolombRiceIntegerEncoding.java b/...m/encoding/GolombRiceIntegerEncoding.java → ...m/encoding/GolombRiceIntegerEncoding.java
diff --git a/...jdk/samtools/cram/encoding/NullCodec.java → ...jdk/samtools/cram/encoding/NullCodec.java b/...jdk/samtools/cram/encoding/NullCodec.java → ...jdk/samtools/cram/encoding/NullCodec.java
diff --git a/.../samtools/cram/encoding/NullEncoding.java → .../samtools/cram/encoding/NullEncoding.java b/.../samtools/cram/encoding/NullEncoding.java → .../samtools/cram/encoding/NullEncoding.java
diff --git a/.../encoding/SubexponentialIntegerCodec.java → .../encoding/SubexponentialIntegerCodec.java b/.../encoding/SubexponentialIntegerCodec.java → .../encoding/SubexponentialIntegerCodec.java
diff --git a/...coding/SubexponentialIntegerEncoding.java → ...coding/SubexponentialIntegerEncoding.java b/...coding/SubexponentialIntegerEncoding.java → ...coding/SubexponentialIntegerEncoding.java
diff --git a/...ls/cram/encoding/huffman/HuffmanCode.java → ...ls/cram/encoding/huffman/HuffmanCode.java b/...ls/cram/encoding/huffman/HuffmanCode.java → ...ls/cram/encoding/huffman/HuffmanCode.java
diff --git a/...ls/cram/encoding/huffman/HuffmanLeaf.java → ...ls/cram/encoding/huffman/HuffmanLeaf.java b/...ls/cram/encoding/huffman/HuffmanLeaf.java → ...ls/cram/encoding/huffman/HuffmanLeaf.java
diff --git a/...ls/cram/encoding/huffman/HuffmanNode.java → ...ls/cram/encoding/huffman/HuffmanNode.java b/...ls/cram/encoding/huffman/HuffmanNode.java → ...ls/cram/encoding/huffman/HuffmanNode.java
diff --git a/...ls/cram/encoding/huffman/HuffmanTree.java → ...ls/cram/encoding/huffman/HuffmanTree.java b/...ls/cram/encoding/huffman/HuffmanTree.java → ...ls/cram/encoding/huffman/HuffmanTree.java
diff --git a/...fman/codec/CanonicalHuffmanByteCodec.java → ...fman/codec/CanonicalHuffmanByteCodec.java b/...fman/codec/CanonicalHuffmanByteCodec.java → ...fman/codec/CanonicalHuffmanByteCodec.java
diff --git a/...n/codec/CanonicalHuffmanIntegerCodec.java → ...n/codec/CanonicalHuffmanIntegerCodec.java b/...n/codec/CanonicalHuffmanIntegerCodec.java → ...n/codec/CanonicalHuffmanIntegerCodec.java
diff --git a/...ncoding/huffman/codec/HuffmanBitCode.java → ...ncoding/huffman/codec/HuffmanBitCode.java b/...ncoding/huffman/codec/HuffmanBitCode.java → ...ncoding/huffman/codec/HuffmanBitCode.java
diff --git a/...ng/huffman/codec/HuffmanByteEncoding.java → ...ng/huffman/codec/HuffmanByteEncoding.java b/...ng/huffman/codec/HuffmanByteEncoding.java → ...ng/huffman/codec/HuffmanByteEncoding.java
diff --git a/...ding/huffman/codec/HuffmanByteHelper.java → ...ding/huffman/codec/HuffmanByteHelper.java b/...ding/huffman/codec/HuffmanByteHelper.java → ...ding/huffman/codec/HuffmanByteHelper.java
diff --git a/...oding/huffman/codec/HuffmanIntHelper.java → ...oding/huffman/codec/HuffmanIntHelper.java b/...oding/huffman/codec/HuffmanIntHelper.java → ...oding/huffman/codec/HuffmanIntHelper.java
diff --git a/...huffman/codec/HuffmanIntegerEncoding.java → ...huffman/codec/HuffmanIntegerEncoding.java b/...huffman/codec/HuffmanIntegerEncoding.java → ...huffman/codec/HuffmanIntegerEncoding.java
diff --git a/...uffman/codec/HuffmanParamsCalculator.java → ...uffman/codec/HuffmanParamsCalculator.java b/...uffman/codec/HuffmanParamsCalculator.java → ...uffman/codec/HuffmanParamsCalculator.java
diff --git a/...amtools/cram/encoding/rans/Constants.java → ...amtools/cram/encoding/rans/Constants.java b/...amtools/cram/encoding/rans/Constants.java → ...amtools/cram/encoding/rans/Constants.java
diff --git a/...sjdk/samtools/cram/encoding/rans/D04.java → ...sjdk/samtools/cram/encoding/rans/D04.java b/...sjdk/samtools/cram/encoding/rans/D04.java → ...sjdk/samtools/cram/encoding/rans/D04.java
diff --git a/...sjdk/samtools/cram/encoding/rans/D14.java → ...sjdk/samtools/cram/encoding/rans/D14.java b/...sjdk/samtools/cram/encoding/rans/D14.java → ...sjdk/samtools/cram/encoding/rans/D14.java
diff --git a/...samtools/cram/encoding/rans/Decoding.java → ...samtools/cram/encoding/rans/Decoding.java b/...samtools/cram/encoding/rans/Decoding.java → ...samtools/cram/encoding/rans/Decoding.java
diff --git a/...sjdk/samtools/cram/encoding/rans/E04.java → ...sjdk/samtools/cram/encoding/rans/E04.java b/...sjdk/samtools/cram/encoding/rans/E04.java → ...sjdk/samtools/cram/encoding/rans/E04.java
diff --git a/...sjdk/samtools/cram/encoding/rans/E14.java → ...sjdk/samtools/cram/encoding/rans/E14.java b/...sjdk/samtools/cram/encoding/rans/E14.java → ...sjdk/samtools/cram/encoding/rans/E14.java
diff --git a/...samtools/cram/encoding/rans/Encoding.java → ...samtools/cram/encoding/rans/Encoding.java b/...samtools/cram/encoding/rans/Encoding.java → ...samtools/cram/encoding/rans/Encoding.java
diff --git a/...tools/cram/encoding/rans/Frequencies.java → ...tools/cram/encoding/rans/Frequencies.java b/...tools/cram/encoding/rans/Frequencies.java → ...tools/cram/encoding/rans/Frequencies.java
diff --git a/...jdk/samtools/cram/encoding/rans/RANS.java → ...jdk/samtools/cram/encoding/rans/RANS.java b/...jdk/samtools/cram/encoding/rans/RANS.java → ...jdk/samtools/cram/encoding/rans/RANS.java
diff --git a/...dk/samtools/cram/encoding/rans/Utils.java → ...dk/samtools/cram/encoding/rans/Utils.java b/...dk/samtools/cram/encoding/rans/Utils.java → ...dk/samtools/cram/encoding/rans/Utils.java
diff --git a/.../cram/encoding/reader/AbstractReader.java → .../cram/encoding/reader/AbstractReader.java b/.../cram/encoding/reader/AbstractReader.java → .../cram/encoding/reader/AbstractReader.java
diff --git a/...ram/encoding/reader/CramRecordReader.java → ...ram/encoding/reader/CramRecordReader.java b/...ram/encoding/reader/CramRecordReader.java → ...ram/encoding/reader/CramRecordReader.java
diff --git a/...ools/cram/encoding/reader/DataReader.java → ...ools/cram/encoding/reader/DataReader.java b/...ools/cram/encoding/reader/DataReader.java → ...ools/cram/encoding/reader/DataReader.java
diff --git a/...am/encoding/reader/DataReaderFactory.java → ...am/encoding/reader/DataReaderFactory.java b/...am/encoding/reader/DataReaderFactory.java → ...am/encoding/reader/DataReaderFactory.java
diff --git a/.../cram/encoding/reader/RefSeqIdReader.java → .../cram/encoding/reader/RefSeqIdReader.java b/.../cram/encoding/reader/RefSeqIdReader.java → .../cram/encoding/reader/RefSeqIdReader.java
diff --git a/...coding/readfeatures/BaseQualityScore.java → ...coding/readfeatures/BaseQualityScore.java b/...coding/readfeatures/BaseQualityScore.java → ...coding/readfeatures/BaseQualityScore.java
diff --git a/...ols/cram/encoding/readfeatures/Bases.java → ...ols/cram/encoding/readfeatures/Bases.java b/...ols/cram/encoding/readfeatures/Bases.java → ...ols/cram/encoding/readfeatures/Bases.java
diff --git a/.../cram/encoding/readfeatures/Deletion.java → .../cram/encoding/readfeatures/Deletion.java b/.../cram/encoding/readfeatures/Deletion.java → .../cram/encoding/readfeatures/Deletion.java
diff --git a/.../cram/encoding/readfeatures/HardClip.java → .../cram/encoding/readfeatures/HardClip.java b/.../cram/encoding/readfeatures/HardClip.java → .../cram/encoding/readfeatures/HardClip.java
diff --git a/...ram/encoding/readfeatures/InsertBase.java → ...ram/encoding/readfeatures/InsertBase.java b/...ram/encoding/readfeatures/InsertBase.java → ...ram/encoding/readfeatures/InsertBase.java
diff --git a/...cram/encoding/readfeatures/Insertion.java → ...cram/encoding/readfeatures/Insertion.java b/...cram/encoding/readfeatures/Insertion.java → ...cram/encoding/readfeatures/Insertion.java
diff --git a/...s/cram/encoding/readfeatures/Padding.java → ...s/cram/encoding/readfeatures/Padding.java b/...s/cram/encoding/readfeatures/Padding.java → ...s/cram/encoding/readfeatures/Padding.java
diff --git a/.../cram/encoding/readfeatures/ReadBase.java → .../cram/encoding/readfeatures/ReadBase.java b/.../cram/encoding/readfeatures/ReadBase.java → .../cram/encoding/readfeatures/ReadBase.java
diff --git a/...am/encoding/readfeatures/ReadFeature.java → ...am/encoding/readfeatures/ReadFeature.java b/...am/encoding/readfeatures/ReadFeature.java → ...am/encoding/readfeatures/ReadFeature.java
diff --git a/...s/cram/encoding/readfeatures/RefSkip.java → ...s/cram/encoding/readfeatures/RefSkip.java b/...s/cram/encoding/readfeatures/RefSkip.java → ...s/cram/encoding/readfeatures/RefSkip.java
diff --git a/...ls/cram/encoding/readfeatures/Scores.java → ...ls/cram/encoding/readfeatures/Scores.java b/...ls/cram/encoding/readfeatures/Scores.java → ...ls/cram/encoding/readfeatures/Scores.java
diff --git a/.../cram/encoding/readfeatures/SoftClip.java → .../cram/encoding/readfeatures/SoftClip.java b/.../cram/encoding/readfeatures/SoftClip.java → .../cram/encoding/readfeatures/SoftClip.java
diff --git a/...m/encoding/readfeatures/Substitution.java → ...m/encoding/readfeatures/Substitution.java b/...m/encoding/readfeatures/Substitution.java → ...m/encoding/readfeatures/Substitution.java
diff --git a/...ools/cram/encoding/writer/DataWriter.java → ...ools/cram/encoding/writer/DataWriter.java b/...ools/cram/encoding/writer/DataWriter.java → ...ools/cram/encoding/writer/DataWriter.java
diff --git a/...am/encoding/writer/DataWriterFactory.java → ...am/encoding/writer/DataWriterFactory.java b/...am/encoding/writer/DataWriterFactory.java → ...am/encoding/writer/DataWriterFactory.java
diff --git a/...samtools/cram/encoding/writer/Writer.java → ...samtools/cram/encoding/writer/Writer.java b/...samtools/cram/encoding/writer/Writer.java → ...samtools/cram/encoding/writer/Writer.java
diff --git a/...sjdk/samtools/cram/io/BitInputStream.java → ...sjdk/samtools/cram/io/BitInputStream.java b/...sjdk/samtools/cram/io/BitInputStream.java → ...sjdk/samtools/cram/io/BitInputStream.java
diff --git a/...jdk/samtools/cram/io/BitOutputStream.java → ...jdk/samtools/cram/io/BitOutputStream.java b/...jdk/samtools/cram/io/BitOutputStream.java → ...jdk/samtools/cram/io/BitOutputStream.java
diff --git a/...dk/samtools/cram/io/CRC32InputStream.java → ...dk/samtools/cram/io/CRC32InputStream.java b/...dk/samtools/cram/io/CRC32InputStream.java → ...dk/samtools/cram/io/CRC32InputStream.java
diff --git a/...k/samtools/cram/io/CRC32OutputStream.java → ...k/samtools/cram/io/CRC32OutputStream.java b/...k/samtools/cram/io/CRC32OutputStream.java → ...k/samtools/cram/io/CRC32OutputStream.java
diff --git a/...samtools/cram/io/CountingInputStream.java → ...samtools/cram/io/CountingInputStream.java b/...samtools/cram/io/CountingInputStream.java → ...samtools/cram/io/CountingInputStream.java
diff --git a/...va/htsjdk/samtools/cram/io/CramArray.java → ...va/htsjdk/samtools/cram/io/CramArray.java b/...va/htsjdk/samtools/cram/io/CramArray.java → ...va/htsjdk/samtools/cram/io/CramArray.java
diff --git a/...java/htsjdk/samtools/cram/io/CramInt.java → ...java/htsjdk/samtools/cram/io/CramInt.java b/...java/htsjdk/samtools/cram/io/CramInt.java → ...java/htsjdk/samtools/cram/io/CramInt.java
diff --git a/...mtools/cram/io/DefaultBitInputStream.java → ...mtools/cram/io/DefaultBitInputStream.java b/...mtools/cram/io/DefaultBitInputStream.java → ...mtools/cram/io/DefaultBitInputStream.java
diff --git a/...tools/cram/io/DefaultBitOutputStream.java → ...tools/cram/io/DefaultBitOutputStream.java b/...tools/cram/io/DefaultBitOutputStream.java → ...tools/cram/io/DefaultBitOutputStream.java
diff --git a/...cram/io/ExposedByteArrayOutputStream.java → ...cram/io/ExposedByteArrayOutputStream.java b/...cram/io/ExposedByteArrayOutputStream.java → ...cram/io/ExposedByteArrayOutputStream.java
diff --git a/...samtools/cram/io/ExternalCompression.java → ...samtools/cram/io/ExternalCompression.java b/...samtools/cram/io/ExternalCompression.java → ...samtools/cram/io/ExternalCompression.java
diff --git a/src/java/htsjdk/samtools/cram/io/ITF8.java → ...in/java/htsjdk/samtools/cram/io/ITF8.java b/src/java/htsjdk/samtools/cram/io/ITF8.java → ...in/java/htsjdk/samtools/cram/io/ITF8.java
diff --git a/...dk/samtools/cram/io/InputStreamUtils.java → ...dk/samtools/cram/io/InputStreamUtils.java b/...dk/samtools/cram/io/InputStreamUtils.java → ...dk/samtools/cram/io/InputStreamUtils.java
diff --git a/src/java/htsjdk/samtools/cram/io/LTF8.java → ...in/java/htsjdk/samtools/cram/io/LTF8.java b/src/java/htsjdk/samtools/cram/io/LTF8.java → ...in/java/htsjdk/samtools/cram/io/LTF8.java
diff --git a/...jdk/samtools/cram/lossy/BaseCategory.java → ...jdk/samtools/cram/lossy/BaseCategory.java b/...jdk/samtools/cram/lossy/BaseCategory.java → ...jdk/samtools/cram/lossy/BaseCategory.java
diff --git a/...samtools/cram/lossy/BaseCategoryType.java → ...samtools/cram/lossy/BaseCategoryType.java b/...samtools/cram/lossy/BaseCategoryType.java → ...samtools/cram/lossy/BaseCategoryType.java
diff --git a/...a/htsjdk/samtools/cram/lossy/Binning.java → ...a/htsjdk/samtools/cram/lossy/Binning.java b/...a/htsjdk/samtools/cram/lossy/Binning.java → ...a/htsjdk/samtools/cram/lossy/Binning.java
diff --git a/...mtools/cram/lossy/PreservationPolicy.java → ...mtools/cram/lossy/PreservationPolicy.java b/...mtools/cram/lossy/PreservationPolicy.java → ...mtools/cram/lossy/PreservationPolicy.java
diff --git a/.../cram/lossy/QualityScorePreservation.java → .../cram/lossy/QualityScorePreservation.java b/.../cram/lossy/QualityScorePreservation.java → .../cram/lossy/QualityScorePreservation.java
diff --git a/...ols/cram/lossy/QualityScoreTreatment.java → ...ols/cram/lossy/QualityScoreTreatment.java b/...ols/cram/lossy/QualityScoreTreatment.java → ...ols/cram/lossy/QualityScoreTreatment.java
diff --git a/...cram/lossy/QualityScoreTreatmentType.java → ...cram/lossy/QualityScoreTreatmentType.java b/...cram/lossy/QualityScoreTreatmentType.java → ...cram/lossy/QualityScoreTreatmentType.java
diff --git a/...jdk/samtools/cram/lossy/ReadCategory.java → ...jdk/samtools/cram/lossy/ReadCategory.java b/...jdk/samtools/cram/lossy/ReadCategory.java → ...jdk/samtools/cram/lossy/ReadCategory.java
diff --git a/...samtools/cram/lossy/ReadCategoryType.java → ...samtools/cram/lossy/ReadCategoryType.java b/...samtools/cram/lossy/ReadCategoryType.java → ...samtools/cram/lossy/ReadCategoryType.java
diff --git a/...amtools/cram/ref/CRAMReferenceSource.java → ...amtools/cram/ref/CRAMReferenceSource.java b/...amtools/cram/ref/CRAMReferenceSource.java → ...amtools/cram/ref/CRAMReferenceSource.java
diff --git a/...sjdk/samtools/cram/ref/EnaRefService.java → ...sjdk/samtools/cram/ref/EnaRefService.java b/...sjdk/samtools/cram/ref/EnaRefService.java → ...sjdk/samtools/cram/ref/EnaRefService.java
diff --git a/...am/ref/InMemoryReferenceSequenceFile.java → ...am/ref/InMemoryReferenceSequenceFile.java b/...am/ref/InMemoryReferenceSequenceFile.java → ...am/ref/InMemoryReferenceSequenceFile.java
diff --git a/...dk/samtools/cram/ref/ReferenceRegion.java → ...dk/samtools/cram/ref/ReferenceRegion.java b/...dk/samtools/cram/ref/ReferenceRegion.java → ...dk/samtools/cram/ref/ReferenceRegion.java
diff --git a/...dk/samtools/cram/ref/ReferenceSource.java → ...dk/samtools/cram/ref/ReferenceSource.java b/...dk/samtools/cram/ref/ReferenceSource.java → ...dk/samtools/cram/ref/ReferenceSource.java
diff --git a/...dk/samtools/cram/ref/ReferenceTracks.java → ...dk/samtools/cram/ref/ReferenceTracks.java b/...dk/samtools/cram/ref/ReferenceTracks.java → ...dk/samtools/cram/ref/ReferenceTracks.java
diff --git a/...amtools/cram/structure/AlignmentSpan.java → ...amtools/cram/structure/AlignmentSpan.java b/...amtools/cram/structure/AlignmentSpan.java → ...amtools/cram/structure/AlignmentSpan.java
diff --git a/...htsjdk/samtools/cram/structure/Block.java → ...htsjdk/samtools/cram/structure/Block.java b/...htsjdk/samtools/cram/structure/Block.java → ...htsjdk/samtools/cram/structure/Block.java
diff --git a/...ram/structure/BlockCompressionMethod.java → ...ram/structure/BlockCompressionMethod.java b/...ram/structure/BlockCompressionMethod.java → ...ram/structure/BlockCompressionMethod.java
diff --git a/...ools/cram/structure/BlockContentType.java → ...ools/cram/structure/BlockContentType.java b/...ools/cram/structure/BlockContentType.java → ...ools/cram/structure/BlockContentType.java
diff --git a/...ols/cram/structure/CompressionHeader.java → ...ols/cram/structure/CompressionHeader.java b/...ols/cram/structure/CompressionHeader.java → ...ols/cram/structure/CompressionHeader.java
diff --git a/...dk/samtools/cram/structure/Container.java → ...dk/samtools/cram/structure/Container.java b/...dk/samtools/cram/structure/Container.java → ...dk/samtools/cram/structure/Container.java
diff --git a/...ols/cram/structure/ContainerHeaderIO.java → ...ols/cram/structure/ContainerHeaderIO.java b/...ols/cram/structure/ContainerHeaderIO.java → ...ols/cram/structure/ContainerHeaderIO.java
diff --git a/.../samtools/cram/structure/ContainerIO.java → .../samtools/cram/structure/ContainerIO.java b/.../samtools/cram/structure/ContainerIO.java → .../samtools/cram/structure/ContainerIO.java
diff --git a/...cram/structure/CramCompressionRecord.java → ...cram/structure/CramCompressionRecord.java b/...cram/structure/CramCompressionRecord.java → ...cram/structure/CramCompressionRecord.java
diff --git a/...k/samtools/cram/structure/CramHeader.java → ...k/samtools/cram/structure/CramHeader.java b/...k/samtools/cram/structure/CramHeader.java → ...k/samtools/cram/structure/CramHeader.java
diff --git a/...k/samtools/cram/structure/EncodingID.java → ...k/samtools/cram/structure/EncodingID.java b/...k/samtools/cram/structure/EncodingID.java → ...k/samtools/cram/structure/EncodingID.java
diff --git a/.../samtools/cram/structure/EncodingKey.java → .../samtools/cram/structure/EncodingKey.java b/.../samtools/cram/structure/EncodingKey.java → .../samtools/cram/structure/EncodingKey.java
diff --git a/...mtools/cram/structure/EncodingParams.java → ...mtools/cram/structure/EncodingParams.java b/...mtools/cram/structure/EncodingParams.java → ...mtools/cram/structure/EncodingParams.java
diff --git a/...sjdk/samtools/cram/structure/ReadTag.java → ...sjdk/samtools/cram/structure/ReadTag.java b/...sjdk/samtools/cram/structure/ReadTag.java → ...sjdk/samtools/cram/structure/ReadTag.java
diff --git a/...htsjdk/samtools/cram/structure/Slice.java → ...htsjdk/samtools/cram/structure/Slice.java b/...htsjdk/samtools/cram/structure/Slice.java → ...htsjdk/samtools/cram/structure/Slice.java
diff --git a/...sjdk/samtools/cram/structure/SliceIO.java → ...sjdk/samtools/cram/structure/SliceIO.java b/...sjdk/samtools/cram/structure/SliceIO.java → ...sjdk/samtools/cram/structure/SliceIO.java
diff --git a/...ls/cram/structure/SubstitutionMatrix.java → ...ls/cram/structure/SubstitutionMatrix.java b/...ls/cram/structure/SubstitutionMatrix.java → ...ls/cram/structure/SubstitutionMatrix.java
diff --git a/...jdk/samtools/example/ExampleSamUsage.java → ...jdk/samtools/example/ExampleSamUsage.java b/...jdk/samtools/example/ExampleSamUsage.java → ...jdk/samtools/example/ExampleSamUsage.java
diff --git a/...k/samtools/example/PrintReadsExample.java → ...k/samtools/example/PrintReadsExample.java b/...k/samtools/example/PrintReadsExample.java → ...k/samtools/example/PrintReadsExample.java
diff --git a/...sjdk/samtools/fastq/AsyncFastqWriter.java → ...sjdk/samtools/fastq/AsyncFastqWriter.java b/...sjdk/samtools/fastq/AsyncFastqWriter.java → ...sjdk/samtools/fastq/AsyncFastqWriter.java
diff --git a/...sjdk/samtools/fastq/BasicFastqWriter.java → ...sjdk/samtools/fastq/BasicFastqWriter.java b/...sjdk/samtools/fastq/BasicFastqWriter.java → ...sjdk/samtools/fastq/BasicFastqWriter.java
diff --git a/...htsjdk/samtools/fastq/FastqConstants.java → ...htsjdk/samtools/fastq/FastqConstants.java b/...htsjdk/samtools/fastq/FastqConstants.java → ...htsjdk/samtools/fastq/FastqConstants.java
diff --git a/...va/htsjdk/samtools/fastq/FastqReader.java → ...va/htsjdk/samtools/fastq/FastqReader.java b/...va/htsjdk/samtools/fastq/FastqReader.java → ...va/htsjdk/samtools/fastq/FastqReader.java
diff --git a/...va/htsjdk/samtools/fastq/FastqRecord.java → ...va/htsjdk/samtools/fastq/FastqRecord.java b/...va/htsjdk/samtools/fastq/FastqRecord.java → ...va/htsjdk/samtools/fastq/FastqRecord.java
diff --git a/...va/htsjdk/samtools/fastq/FastqWriter.java → ...va/htsjdk/samtools/fastq/FastqWriter.java b/...va/htsjdk/samtools/fastq/FastqWriter.java → ...va/htsjdk/samtools/fastq/FastqWriter.java
diff --git a/...dk/samtools/fastq/FastqWriterFactory.java → ...dk/samtools/fastq/FastqWriterFactory.java b/...dk/samtools/fastq/FastqWriterFactory.java → ...dk/samtools/fastq/FastqWriterFactory.java
diff --git a/...ools/filter/AbstractJavascriptFilter.java → ...ools/filter/AbstractJavascriptFilter.java b/...ools/filter/AbstractJavascriptFilter.java → ...ools/filter/AbstractJavascriptFilter.java
diff --git a/...sjdk/samtools/filter/AggregateFilter.java → ...sjdk/samtools/filter/AggregateFilter.java b/...sjdk/samtools/filter/AggregateFilter.java → ...sjdk/samtools/filter/AggregateFilter.java
diff --git a/...htsjdk/samtools/filter/AlignedFilter.java → ...htsjdk/samtools/filter/AlignedFilter.java b/...htsjdk/samtools/filter/AlignedFilter.java → ...htsjdk/samtools/filter/AlignedFilter.java
diff --git a/.../samtools/filter/DuplicateReadFilter.java → .../samtools/filter/DuplicateReadFilter.java b/.../samtools/filter/DuplicateReadFilter.java → .../samtools/filter/DuplicateReadFilter.java
diff --git a/.../filter/FailsVendorReadQualityFilter.java → .../filter/FailsVendorReadQualityFilter.java b/.../filter/FailsVendorReadQualityFilter.java → .../filter/FailsVendorReadQualityFilter.java
diff --git a/...dk/samtools/filter/FilteringIterator.java → ...dk/samtools/filter/FilteringIterator.java b/...dk/samtools/filter/FilteringIterator.java → ...dk/samtools/filter/FilteringIterator.java
diff --git a/...samtools/filter/FilteringSamIterator.java → ...samtools/filter/FilteringSamIterator.java b/...samtools/filter/FilteringSamIterator.java → ...samtools/filter/FilteringSamIterator.java
diff --git a/...jdk/samtools/filter/InsertSizeFilter.java → ...jdk/samtools/filter/InsertSizeFilter.java b/...jdk/samtools/filter/InsertSizeFilter.java → ...jdk/samtools/filter/InsertSizeFilter.java
diff --git a/...tsjdk/samtools/filter/IntervalFilter.java → ...tsjdk/samtools/filter/IntervalFilter.java b/...tsjdk/samtools/filter/IntervalFilter.java → ...tsjdk/samtools/filter/IntervalFilter.java
diff --git a/...ols/filter/JavascriptSamRecordFilter.java → ...ols/filter/JavascriptSamRecordFilter.java b/...ols/filter/JavascriptSamRecordFilter.java → ...ols/filter/JavascriptSamRecordFilter.java
diff --git a/...samtools/filter/MappingQualityFilter.java → ...samtools/filter/MappingQualityFilter.java b/...samtools/filter/MappingQualityFilter.java → ...samtools/filter/MappingQualityFilter.java
diff --git a/...ols/filter/NotPrimaryAlignmentFilter.java → ...ols/filter/NotPrimaryAlignmentFilter.java b/...ols/filter/NotPrimaryAlignmentFilter.java → ...ols/filter/NotPrimaryAlignmentFilter.java
diff --git a/...amtools/filter/OverclippedReadFilter.java → ...amtools/filter/OverclippedReadFilter.java b/...amtools/filter/OverclippedReadFilter.java → ...amtools/filter/OverclippedReadFilter.java
diff --git a/...tsjdk/samtools/filter/ReadNameFilter.java → ...tsjdk/samtools/filter/ReadNameFilter.java b/...tsjdk/samtools/filter/ReadNameFilter.java → ...tsjdk/samtools/filter/ReadNameFilter.java
diff --git a/...sjdk/samtools/filter/SamRecordFilter.java → ...sjdk/samtools/filter/SamRecordFilter.java b/...sjdk/samtools/filter/SamRecordFilter.java → ...sjdk/samtools/filter/SamRecordFilter.java
diff --git a/...ools/filter/SecondaryAlignmentFilter.java → ...ools/filter/SecondaryAlignmentFilter.java b/...ools/filter/SecondaryAlignmentFilter.java → ...ools/filter/SecondaryAlignmentFilter.java
diff --git a/...ilter/SecondaryOrSupplementaryFilter.java → ...ilter/SecondaryOrSupplementaryFilter.java b/...ilter/SecondaryOrSupplementaryFilter.java → ...ilter/SecondaryOrSupplementaryFilter.java
diff --git a/...dk/samtools/filter/SolexaNoiseFilter.java → ...dk/samtools/filter/SolexaNoiseFilter.java b/...dk/samtools/filter/SolexaNoiseFilter.java → ...dk/samtools/filter/SolexaNoiseFilter.java