Basic reorganization of tree

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@8 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 15:28:56 +00:00 · 2009-02-28 15:28:56 +00:00 · 17aabb38f9
parent c9f0161e24
commit 17aabb38f9
246 changed files with 4054 additions and 0 deletions
--- a/data/gFFTest.gff
+++ b/data/gFFTest.gff
@ -0,0 +1,7 @@
 SEQ1	EMBL	atg	103	105	.	+	0
 SEQ1	EMBL	exon	103	172	.	+	0
 SEQ1	EMBL	splice5	172	173	.	+	.
 SEQ1	netgene	splice5	172	173	0.94	+	.
 SEQ1	genie	sp5-20	163	182	2.3	+	.
 SEQ1	genie	sp5-10	168	177	2.1	+	.
 SEQ2	grail	ATG	17	19	2.1	-	0
--- a/java/lib/edu/mit/broad/arachne/Alignment.java
+++ b/java/lib/edu/mit/broad/arachne/Alignment.java
--- a/java/lib/edu/mit/broad/arachne/Fastb2Fasta.java
+++ b/java/lib/edu/mit/broad/arachne/Fastb2Fasta.java
--- a/java/lib/edu/mit/broad/arachne/FastbReader.java
+++ b/java/lib/edu/mit/broad/arachne/FastbReader.java
--- a/java/lib/edu/mit/broad/arachne/GenomeMask.java
+++ b/java/lib/edu/mit/broad/arachne/GenomeMask.java
--- a/java/lib/edu/mit/broad/arachne/LookAlignReader.java
+++ b/java/lib/edu/mit/broad/arachne/LookAlignReader.java
--- a/java/lib/edu/mit/broad/cnv/AnalyzeCnvs.java
+++ b/java/lib/edu/mit/broad/cnv/AnalyzeCnvs.java
--- a/java/lib/edu/mit/broad/cnv/CountAlignments.java
+++ b/java/lib/edu/mit/broad/cnv/CountAlignments.java
--- a/java/lib/edu/mit/broad/cnv/CountKMers.java
+++ b/java/lib/edu/mit/broad/cnv/CountKMers.java
--- a/java/lib/edu/mit/broad/cnv/CountKMers3.java
+++ b/java/lib/edu/mit/broad/cnv/CountKMers3.java
--- a/java/lib/edu/mit/broad/cnv/GatherAlignments.java
+++ b/java/lib/edu/mit/broad/cnv/GatherAlignments.java
--- a/java/lib/edu/mit/broad/cnv/kmer/CountKMers.java
+++ b/java/lib/edu/mit/broad/cnv/kmer/CountKMers.java
--- a/java/lib/edu/mit/broad/cnv/kmer/DistributedKMerCounter.java
+++ b/java/lib/edu/mit/broad/cnv/kmer/DistributedKMerCounter.java
--- a/java/lib/edu/mit/broad/cnv/util/GenomeBaseIndex.java
+++ b/java/lib/edu/mit/broad/cnv/util/GenomeBaseIndex.java
--- a/java/lib/edu/mit/broad/cnv/util/GenomeBinIndex.java
+++ b/java/lib/edu/mit/broad/cnv/util/GenomeBinIndex.java
--- a/java/lib/edu/mit/broad/cnv/util/SequenceIterator.java
+++ b/java/lib/edu/mit/broad/cnv/util/SequenceIterator.java
--- a/java/lib/edu/mit/broad/dcp/CallStatus.java
+++ b/java/lib/edu/mit/broad/dcp/CallStatus.java
--- a/java/lib/edu/mit/broad/dcp/CommandRunner.java
+++ b/java/lib/edu/mit/broad/dcp/CommandRunner.java
--- a/java/lib/edu/mit/broad/dcp/DistributedAlgorithm.java
+++ b/java/lib/edu/mit/broad/dcp/DistributedAlgorithm.java
--- a/java/lib/edu/mit/broad/dcp/DistributedAlgorithmWorker.java
+++ b/java/lib/edu/mit/broad/dcp/DistributedAlgorithmWorker.java
--- a/java/lib/edu/mit/broad/dcp/DistributedCallServer.java
+++ b/java/lib/edu/mit/broad/dcp/DistributedCallServer.java
--- a/java/lib/edu/mit/broad/dcp/DistributedCallService.java
+++ b/java/lib/edu/mit/broad/dcp/DistributedCallService.java
--- a/java/lib/edu/mit/broad/dcp/message/DistributedCallMessage.java
+++ b/java/lib/edu/mit/broad/dcp/message/DistributedCallMessage.java
--- a/java/lib/edu/mit/broad/dcp/message/DistributedMessage.java
+++ b/java/lib/edu/mit/broad/dcp/message/DistributedMessage.java
--- a/java/lib/edu/mit/broad/picard/PicardException.java
+++ b/java/lib/edu/mit/broad/picard/PicardException.java
--- a/java/lib/edu/mit/broad/picard/aligner/AbstractBaseAligner.java
+++ b/java/lib/edu/mit/broad/picard/aligner/AbstractBaseAligner.java
--- a/java/lib/edu/mit/broad/picard/aligner/Aligner.java
+++ b/java/lib/edu/mit/broad/picard/aligner/Aligner.java
--- a/java/lib/edu/mit/broad/picard/aligner/maq/BamToBfqWriter.java
+++ b/java/lib/edu/mit/broad/picard/aligner/maq/BamToBfqWriter.java
--- a/java/lib/edu/mit/broad/picard/aligner/maq/MapFileIterator.java
+++ b/java/lib/edu/mit/broad/picard/aligner/maq/MapFileIterator.java
--- a/java/lib/edu/mit/broad/picard/aligner/maq/MaqAligner.java
+++ b/java/lib/edu/mit/broad/picard/aligner/maq/MaqAligner.java
--- a/java/lib/edu/mit/broad/picard/aligner/maq/MaqConstants.java
+++ b/java/lib/edu/mit/broad/picard/aligner/maq/MaqConstants.java
--- a/java/lib/edu/mit/broad/picard/aligner/maq/MaqMapMerger.java
+++ b/java/lib/edu/mit/broad/picard/aligner/maq/MaqMapMerger.java
--- a/java/lib/edu/mit/broad/picard/aligner/maq/RunMaq.java
+++ b/java/lib/edu/mit/broad/picard/aligner/maq/RunMaq.java
--- a/java/lib/edu/mit/broad/picard/cmdline/CommandLineParseException.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/CommandLineParseException.java
--- a/java/lib/edu/mit/broad/picard/cmdline/CommandLineParser.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/CommandLineParser.java
--- a/java/lib/edu/mit/broad/picard/cmdline/CommandLineParserDefinitionException.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/CommandLineParserDefinitionException.java
--- a/java/lib/edu/mit/broad/picard/cmdline/CommandLineProgram.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/CommandLineProgram.java
--- a/java/lib/edu/mit/broad/picard/cmdline/CommandLineUtils.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/CommandLineUtils.java
--- a/java/lib/edu/mit/broad/picard/cmdline/Option.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/Option.java
--- a/java/lib/edu/mit/broad/picard/cmdline/PositionalArguments.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/PositionalArguments.java
--- a/java/lib/edu/mit/broad/picard/cmdline/Usage.java
+++ b/java/lib/edu/mit/broad/picard/cmdline/Usage.java
--- a/java/lib/edu/mit/broad/picard/directed/ArachneMapToIntervalList.java
+++ b/java/lib/edu/mit/broad/picard/directed/ArachneMapToIntervalList.java
--- a/java/lib/edu/mit/broad/picard/directed/CalculateHsMetrics.java
+++ b/java/lib/edu/mit/broad/picard/directed/CalculateHsMetrics.java
--- a/java/lib/edu/mit/broad/picard/directed/GenomeMask.java
+++ b/java/lib/edu/mit/broad/picard/directed/GenomeMask.java
--- a/java/lib/edu/mit/broad/picard/directed/GenomeMaskFactory.java
+++ b/java/lib/edu/mit/broad/picard/directed/GenomeMaskFactory.java
--- a/java/lib/edu/mit/broad/picard/directed/HsMetrics.java
+++ b/java/lib/edu/mit/broad/picard/directed/HsMetrics.java
--- a/java/lib/edu/mit/broad/picard/directed/HsMetricsCalculator.java
+++ b/java/lib/edu/mit/broad/picard/directed/HsMetricsCalculator.java
--- a/java/lib/edu/mit/broad/picard/directed/IntervalList.java
+++ b/java/lib/edu/mit/broad/picard/directed/IntervalList.java
--- a/java/lib/edu/mit/broad/picard/filter/AggregateFilter.java
+++ b/java/lib/edu/mit/broad/picard/filter/AggregateFilter.java
--- a/java/lib/edu/mit/broad/picard/filter/FailsVendorReadQualityFilter.java
+++ b/java/lib/edu/mit/broad/picard/filter/FailsVendorReadQualityFilter.java
--- a/java/lib/edu/mit/broad/picard/filter/FilteringIterator.java
+++ b/java/lib/edu/mit/broad/picard/filter/FilteringIterator.java
--- a/java/lib/edu/mit/broad/picard/filter/SamRecordFilter.java
+++ b/java/lib/edu/mit/broad/picard/filter/SamRecordFilter.java
--- a/java/lib/edu/mit/broad/picard/filter/SolexaNoiseFilter.java
+++ b/java/lib/edu/mit/broad/picard/filter/SolexaNoiseFilter.java
--- a/java/lib/edu/mit/broad/picard/filter/TagFilter.java
+++ b/java/lib/edu/mit/broad/picard/filter/TagFilter.java
--- a/java/lib/edu/mit/broad/picard/genotype/GeliException.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GeliException.java
--- a/java/lib/edu/mit/broad/picard/genotype/GeliFileConstants.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GeliFileConstants.java
--- a/java/lib/edu/mit/broad/picard/genotype/GeliFileReader.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GeliFileReader.java
--- a/java/lib/edu/mit/broad/picard/genotype/GeliFileReaderImplementation.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GeliFileReaderImplementation.java
--- a/java/lib/edu/mit/broad/picard/genotype/GeliFileWriter.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GeliFileWriter.java
--- a/java/lib/edu/mit/broad/picard/genotype/GenotypeLikelihoods.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GenotypeLikelihoods.java
--- a/java/lib/edu/mit/broad/picard/genotype/GenotypeLikelihoodsCodec.java
+++ b/java/lib/edu/mit/broad/picard/genotype/GenotypeLikelihoodsCodec.java
--- a/java/lib/edu/mit/broad/picard/genotype/caller/AbstractAlleleCaller.java
+++ b/java/lib/edu/mit/broad/picard/genotype/caller/AbstractAlleleCaller.java
--- a/java/lib/edu/mit/broad/picard/genotype/caller/CallGenotypes.java
+++ b/java/lib/edu/mit/broad/picard/genotype/caller/CallGenotypes.java
--- a/java/lib/edu/mit/broad/picard/genotype/caller/DiploidGenotype.java
+++ b/java/lib/edu/mit/broad/picard/genotype/caller/DiploidGenotype.java
--- a/java/lib/edu/mit/broad/picard/genotype/caller/FlatQualityAlleleCaller.java
+++ b/java/lib/edu/mit/broad/picard/genotype/caller/FlatQualityAlleleCaller.java
--- a/java/lib/edu/mit/broad/picard/genotype/caller/GenotypeTheory.java
+++ b/java/lib/edu/mit/broad/picard/genotype/caller/GenotypeTheory.java
--- a/java/lib/edu/mit/broad/picard/genotype/caller/QualityScoreAlleleCaller.java
+++ b/java/lib/edu/mit/broad/picard/genotype/caller/QualityScoreAlleleCaller.java
--- a/java/lib/edu/mit/broad/picard/illumina/BustardFileParser.java
+++ b/java/lib/edu/mit/broad/picard/illumina/BustardFileParser.java
--- a/java/lib/edu/mit/broad/picard/illumina/BustardFilenameComparator.java
+++ b/java/lib/edu/mit/broad/picard/illumina/BustardFilenameComparator.java
--- a/java/lib/edu/mit/broad/picard/illumina/BustardReadData.java
+++ b/java/lib/edu/mit/broad/picard/illumina/BustardReadData.java
--- a/java/lib/edu/mit/broad/picard/illumina/BustardToSam.java
+++ b/java/lib/edu/mit/broad/picard/illumina/BustardToSam.java
--- a/java/lib/edu/mit/broad/picard/illumina/BustardToSamWriter.java
+++ b/java/lib/edu/mit/broad/picard/illumina/BustardToSamWriter.java
--- a/java/lib/edu/mit/broad/picard/illumina/GeraldParser.java
+++ b/java/lib/edu/mit/broad/picard/illumina/GeraldParser.java
--- a/java/lib/edu/mit/broad/picard/illumina/GeraldParserFactory.java
+++ b/java/lib/edu/mit/broad/picard/illumina/GeraldParserFactory.java
--- a/java/lib/edu/mit/broad/picard/illumina/GeraldToSam.java
+++ b/java/lib/edu/mit/broad/picard/illumina/GeraldToSam.java
--- a/java/lib/edu/mit/broad/picard/illumina/SimpleMapping.java
+++ b/java/lib/edu/mit/broad/picard/illumina/SimpleMapping.java
--- a/java/lib/edu/mit/broad/picard/illumina/SolexaQualityConverter.java
+++ b/java/lib/edu/mit/broad/picard/illumina/SolexaQualityConverter.java
--- a/java/lib/edu/mit/broad/picard/illumina/SquashedCoordinateMap.java
+++ b/java/lib/edu/mit/broad/picard/illumina/SquashedCoordinateMap.java
--- a/java/lib/edu/mit/broad/picard/importer/genotype/BedFileReader.java
+++ b/java/lib/edu/mit/broad/picard/importer/genotype/BedFileReader.java
--- a/java/lib/edu/mit/broad/picard/importer/genotype/BedToGeli.java
+++ b/java/lib/edu/mit/broad/picard/importer/genotype/BedToGeli.java
--- a/java/lib/edu/mit/broad/picard/importer/genotype/SNP.java
+++ b/java/lib/edu/mit/broad/picard/importer/genotype/SNP.java
--- a/java/lib/edu/mit/broad/picard/io/IoUtil.java
+++ b/java/lib/edu/mit/broad/picard/io/IoUtil.java
--- a/java/lib/edu/mit/broad/picard/metrics/AggregateMetricCollector.java
+++ b/java/lib/edu/mit/broad/picard/metrics/AggregateMetricCollector.java
--- a/java/lib/edu/mit/broad/picard/metrics/Header.java
+++ b/java/lib/edu/mit/broad/picard/metrics/Header.java
--- a/java/lib/edu/mit/broad/picard/metrics/MetricBase.java
+++ b/java/lib/edu/mit/broad/picard/metrics/MetricBase.java
--- a/java/lib/edu/mit/broad/picard/metrics/MetricCollector.java
+++ b/java/lib/edu/mit/broad/picard/metrics/MetricCollector.java
--- a/java/lib/edu/mit/broad/picard/metrics/MetricsFile.java
+++ b/java/lib/edu/mit/broad/picard/metrics/MetricsFile.java
--- a/java/lib/edu/mit/broad/picard/metrics/StringHeader.java
+++ b/java/lib/edu/mit/broad/picard/metrics/StringHeader.java
--- a/java/lib/edu/mit/broad/picard/metrics/VersionHeader.java
+++ b/java/lib/edu/mit/broad/picard/metrics/VersionHeader.java
--- a/java/lib/edu/mit/broad/picard/quality/CalibrateQualityScores.java
+++ b/java/lib/edu/mit/broad/picard/quality/CalibrateQualityScores.java
--- a/java/lib/edu/mit/broad/picard/quality/QualityScoreCalibrator.java
+++ b/java/lib/edu/mit/broad/picard/quality/QualityScoreCalibrator.java
--- a/java/lib/edu/mit/broad/picard/quality/QualityScoreMatrix.java
+++ b/java/lib/edu/mit/broad/picard/quality/QualityScoreMatrix.java
--- a/java/lib/edu/mit/broad/picard/reference/FastaSequenceFile.java
+++ b/java/lib/edu/mit/broad/picard/reference/FastaSequenceFile.java
--- a/java/lib/edu/mit/broad/picard/reference/ReferenceSequence.java
+++ b/java/lib/edu/mit/broad/picard/reference/ReferenceSequence.java
--- a/java/lib/edu/mit/broad/picard/reference/ReferenceSequenceFile.java
+++ b/java/lib/edu/mit/broad/picard/reference/ReferenceSequenceFile.java
--- a/java/lib/edu/mit/broad/picard/reference/ReferenceSequenceFileFactory.java
+++ b/java/lib/edu/mit/broad/picard/reference/ReferenceSequenceFileFactory.java
--- a/java/lib/edu/mit/broad/picard/sam/CollectAlignmentSummaryMetrics.java
+++ b/java/lib/edu/mit/broad/picard/sam/CollectAlignmentSummaryMetrics.java
--- a/java/lib/edu/mit/broad/picard/sam/CollectInsertSizeMetrics.java
+++ b/java/lib/edu/mit/broad/picard/sam/CollectInsertSizeMetrics.java
--- a/java/lib/edu/mit/broad/picard/sam/ComparableSamRecordIterator.java
+++ b/java/lib/edu/mit/broad/picard/sam/ComparableSamRecordIterator.java
--- a/java/lib/edu/mit/broad/picard/sam/CreateSequenceDictionary.java
+++ b/java/lib/edu/mit/broad/picard/sam/CreateSequenceDictionary.java
--- a/Show More
+++ b/Show More