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Updated picard jars. They did a big package rearrangement so had to modify a bunch of classes. Might be a bit painful to get stuff fixed.

biotelerock 2014-05-28

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Parent: [r237]

Child: [r239]

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added /trunk/LibraryJars/htsjdk-1.114.jar
added /trunk/LibraryJars/picard-1.114.jar
changed /trunk/Misc/JavaxComOrgInfoNetClasses.zip
added /trunk/Misc/OldJavaxComOrgInfoNetClasses.zip
changed /trunk/Source/edu/utah/ames/bioinfo/PicardMarkDuplicates.java
changed /trunk/Source/edu/utah/diagnostics/CountChromosomes.java
changed /trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java
changed /trunk/Source/edu/utah/seq/analysis/AWDefinedRegionDifferentialSeq.java
changed /trunk/Source/edu/utah/seq/analysis/AllelicMethylationDetector.java
changed /trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java
changed /trunk/Source/edu/utah/seq/analysis/OverdispersedRegionScanSeqs.java
changed /trunk/Source/edu/utah/seq/analysis/PullMatchingAlignments.java
changed /trunk/Source/edu/utah/seq/analysis/RNASeq.java
changed /trunk/Source/edu/utah/seq/analysis/ScoreEnrichedRegions.java
changed /trunk/Source/edu/utah/seq/analysis/multi/Replica.java
changed /trunk/Source/edu/utah/seq/base/BamIntensityJoiner.java
changed /trunk/Source/edu/utah/seq/base/BamNMerIntensityParser.java
changed /trunk/Source/edu/utah/seq/base/BaseClassifier.java
changed /trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java
changed /trunk/Source/edu/utah/seq/base/VariantAlignment.java
changed /trunk/Source/edu/utah/seq/data/Bam2Bar.java
changed /trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java
changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed /trunk/Source/edu/utah/seq/data/SamReadDepthSubSampler.java
changed /trunk/Source/edu/utah/seq/data/SamSVFilter.java
/trunk/LibraryJars/htsjdk-1.114.jar
Binary file was added.
/trunk/LibraryJars/picard-1.114.jar
Binary file was added.
/trunk/Misc/JavaxComOrgInfoNetClasses.zip
Binary file was changed.
/trunk/Misc/OldJavaxComOrgInfoNetClasses.zip
Binary file was added.
/trunk/Source/edu/utah/ames/bioinfo/PicardMarkDuplicates.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/diagnostics/CountChromosomes.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/AWDefinedRegionDifferentialSeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/AllelicMethylationDetector.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/OverdispersedRegionScanSeqs.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/PullMatchingAlignments.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/RNASeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/ScoreEnrichedRegions.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/multi/Replica.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/BamIntensityJoiner.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/BamNMerIntensityParser.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/BaseClassifier.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/VariantAlignment.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/Bam2Bar.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/SamReadDepthSubSampler.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/SamSVFilter.java Diff Switch to side-by-side view
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