USeq Source Code

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Commit [r131] Maximize Restore History

edu.utah.tomato: lots of fixes and improvements

edu.utah.seq.vcf: Added automatic vcf chunking to improve memory usage
edu.utah.diagnostics: Metrics are now reported as html and can be merged. Fixed figures.
edu.utah.seq.data: Fixed error in CalculatePerCycleErrorRate. Only encountered when the number of phiX sequences is huge.

Authored by: tmosbruger 2013-06-26

Browse code at this revision

Parent: [r130]

Child: [r132]

changed	/trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java
added	/trunk/Source/edu/utah/diagnostics/MergeExonMetrics.java
changed	/trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java
changed	/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.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/VCFParser.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFReporter.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFUtilities.java
changed	/trunk/Source/edu/utah/tomato/TFCommand.java
changed	/trunk/Source/edu/utah/tomato/TFCommandExomeAlign.java
changed	/trunk/Source/edu/utah/tomato/TFCommandExomeMetrics.java
changed	/trunk/Source/edu/utah/tomato/TFCommandExomeVariantRaw.java
changed	/trunk/Source/edu/utah/tomato/TFConstants.java
changed	/trunk/Source/edu/utah/tomato/TomatoFarmer.java
changed	/trunk/build.properties

/trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/MergeExonMetrics.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java Diff Switch to side-by-side view

USeq Source Code

Commit [r131] Maximize Restore History

/trunk/Source/edu/utah/diagnostics/GenerateOverlapStats.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/MergeExonMetrics.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFReporter.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFUtilities.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/tomato/TFCommand.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/tomato/TFCommandExomeAlign.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/tomato/TFCommandExomeMetrics.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/tomato/TFCommandExomeVariantRaw.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/tomato/TFConstants.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/tomato/TomatoFarmer.java Diff Switch to side-by-side view

/trunk/build.properties Diff Switch to side-by-side view