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Viewing all changes in revision 6.

Committer: Bazaar Package Importer
Author(s): Shaun Jackman
Date: 2010-07-28 16:22:20 UTC
mfrom: (1.1.4 upstream)
Revision ID: james.westby@ubuntu.com-20100728162220-52jfb2bsl9v7u520

Tags: 1.5.14-1

* New upstream release.
* Remove libcolt-java from the dependencies.
* Bump Standards-Version to 3.9.1.

files added:
src/org/broad/igv/util/collections

src/org/broad/igv/util/collections/DoubleArrayList.java

src/org/broad/igv/util/collections/FloatArrayList.java

src/org/broad/igv/util/collections/IntArrayList.java

src/org/broad/tribble/util/LittleEndianInputStream.java

src/org/broad/tribble/util/LittleEndianOutputStream.java

files removed:
src/org/broad/tribble/util/LEDataInputStream.java

src/org/broad/tribble/util/LEDataOutputStream.java

files modified:
.pc/01-build.xml/build.xml

build.xml

debian/changelog

debian/control

debian/patches/01-build.xml

src/org/broad/igv/data/AbstractDataSource.java

src/org/broad/igv/data/GCTDatasetParser.java

src/org/broad/igv/data/GenomeSummaryData.java

src/org/broad/igv/data/IGVDatasetParser.java

src/org/broad/igv/data/ProcessingUtils.java

src/org/broad/igv/data/WiggleDataset.java

src/org/broad/igv/data/WiggleParser.java

src/org/broad/igv/feature/AbstractFeatureParser.java

src/org/broad/igv/feature/EmblFeatureTableParser.java

src/org/broad/igv/feature/FeatureParser.java

src/org/broad/igv/feature/GFFParser.java

src/org/broad/igv/feature/GeneManager.java

src/org/broad/igv/feature/GenomeImporter.java

src/org/broad/igv/feature/MutationParser.java

src/org/broad/igv/feature/ProbeToGeneMap.java

src/org/broad/igv/feature/dranger/DRangerRenderer.java

src/org/broad/igv/renderer/XYPlotRenderer.java

src/org/broad/igv/sam/EWigTrack.java

src/org/broad/igv/session/SessionReader.java

src/org/broad/igv/session/SessionWriter.java

src/org/broad/igv/tdf/Bin.java

src/org/broad/igv/tdf/TDFReader.java

src/org/broad/igv/tools/Accumulator.java

src/org/broad/igv/tools/IgvTools.java

src/org/broad/igv/tools/Preprocessor.java

src/org/broad/igv/tools/parsers/GCTParser.java

src/org/broad/igv/track/AbstractTrack.java

src/org/broad/igv/track/DataTrack.java

src/org/broad/igv/track/TrackLoader.java

src/org/broad/igv/track/TrackManager.java

src/org/broad/igv/track/TrackProperties.java

src/org/broad/igv/track/tribble/BEDCodec.java

src/org/broad/igv/track/tribble/CodecFactory.java

src/org/broad/igv/track/tribble/VCFCodec.java

src/org/broad/igv/track/tribble/VCFFeature.java

src/org/broad/igv/ui/IGVCommandBar.java

src/org/broad/igv/ui/ResourceTree.java

src/org/broad/igv/util/ColorUtilities.java

src/org/broad/igv/util/ParsingUtils.java

src/org/broad/igv/util/ResourceLocator.java

src/org/broad/igv/util/SeekableStream.java

src/org/broad/igv/util/StreamUtils.java

src/org/broad/igv/util/StringUtils.java

src/org/broad/tribble/index/AbstractIndex.java

src/org/broad/tribble/index/ChrIndex.java

src/org/broad/tribble/index/Index.java

src/org/broad/tribble/index/IndexFactory.java

src/org/broad/tribble/index/interval/IntervalTreeIndex.java

src/org/broad/tribble/index/linear/LinearIndex.java

src/org/broad/tribble/readers/TabixReader.java

src/resources/about.properties

Show diffs side-by-side

added added

removed removed

.pc/01-build.xml/build.xml

debian/changelog

debian/patches/01-build.xml

src/org/broad/igv/data/AbstractDataSource.java

src/org/broad/igv/data/GCTDatasetParser.java

src/org/broad/igv/data/GenomeSummaryData.java

src/org/broad/igv/data/IGVDatasetParser.java

src/org/broad/igv/data/ProcessingUtils.java

src/org/broad/igv/data/WiggleDataset.java

src/org/broad/igv/data/WiggleParser.java

src/org/broad/igv/feature/AbstractFeatureParser.java

src/org/broad/igv/feature/EmblFeatureTableParser.java

src/org/broad/igv/feature/FeatureParser.java

src/org/broad/igv/feature/GFFParser.java

src/org/broad/igv/feature/GeneManager.java

src/org/broad/igv/feature/GenomeImporter.java

src/org/broad/igv/feature/MutationParser.java

src/org/broad/igv/feature/ProbeToGeneMap.java

src/org/broad/igv/feature/dranger/DRangerRenderer.java

src/org/broad/igv/renderer/XYPlotRenderer.java

src/org/broad/igv/sam/EWigTrack.java

src/org/broad/igv/session/SessionReader.java

src/org/broad/igv/session/SessionWriter.java

src/org/broad/igv/tdf/Bin.java

src/org/broad/igv/tdf/TDFReader.java

src/org/broad/igv/tools/Accumulator.java

src/org/broad/igv/tools/IgvTools.java

src/org/broad/igv/tools/Preprocessor.java

src/org/broad/igv/tools/parsers/GCTParser.java

src/org/broad/igv/track/AbstractTrack.java

src/org/broad/igv/track/DataTrack.java

src/org/broad/igv/track/TrackLoader.java

src/org/broad/igv/track/TrackManager.java

src/org/broad/igv/track/TrackProperties.java

src/org/broad/igv/track/tribble/BEDCodec.java

src/org/broad/igv/track/tribble/CodecFactory.java

src/org/broad/igv/track/tribble/VCFCodec.java

src/org/broad/igv/track/tribble/VCFFeature.java

src/org/broad/igv/ui/IGVCommandBar.java

src/org/broad/igv/ui/ResourceTree.java

src/org/broad/igv/util/ColorUtilities.java

src/org/broad/igv/util/ParsingUtils.java

src/org/broad/igv/util/ResourceLocator.java

src/org/broad/igv/util/SeekableStream.java

src/org/broad/igv/util/StreamUtils.java

src/org/broad/igv/util/StringUtils.java

src/org/broad/igv/util/collections/

src/org/broad/igv/util/collections/DoubleArrayList.java

src/org/broad/igv/util/collections/FloatArrayList.java

src/org/broad/igv/util/collections/IntArrayList.java

src/org/broad/tribble/index/AbstractIndex.java

src/org/broad/tribble/index/ChrIndex.java

src/org/broad/tribble/index/Index.java

src/org/broad/tribble/index/IndexFactory.java

src/org/broad/tribble/index/interval/IntervalTreeIndex.java

src/org/broad/tribble/index/linear/LinearIndex.java

src/org/broad/tribble/readers/TabixReader.java

src/org/broad/tribble/util/LEDataInputStream.java

src/org/broad/tribble/util/LEDataOutputStream.java

src/org/broad/tribble/util/LittleEndianInputStream.java

src/org/broad/tribble/util/LittleEndianOutputStream.java

src/resources/about.properties

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