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Commit [r119]  Maximize  Restore  History

Fixes and Improvements to the variation pipeline

tmosbruger 2013-06-02

changed /trunk/Source/edu/utah/diagnostics/CountChromosomes.java
changed /trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java
changed /trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java
changed /trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java
changed /trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java
changed /trunk/Source/edu/utah/seq/vcf/VCFRecord.java
changed /trunk/Source/edu/utah/seq/vcf/VCFReporter.java
changed /trunk/Source/edu/utah/seq/vcf/VCFUtilities.java
/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/diagnostics/ParseExonMetrics.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFRecord.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFReporter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFUtilities.java Diff Switch to side-by-side view
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