USeq / Source Code / Commit [r271]

Commit [r271] Maximize Restore History

Lots of mods....

Authored by: biotelerock 2014-11-25

Browse code at this revision

Parent: [r270]

Child: [r272]

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changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
added	/trunk/LibraryJars/poi-3.10.1-20140818.jar
added	/trunk/LibraryJars/poi-ooxml-3.10.1-20140818.jar
added	/trunk/LibraryJars/poi-ooxml-schemas-3.10.1-20140818.jar
changed	/trunk/Source/edu/utah/seq/analysis/AggregatePlotter.java
added	/trunk/Source/edu/utah/seq/analysis/AllelicExpressionComparator.java
changed	/trunk/Source/edu/utah/seq/analysis/AllelicExpressionDetector.java
added	/trunk/Source/edu/utah/seq/analysis/AllelicExpressionSnp.java
changed	/trunk/Source/edu/utah/seq/analysis/BisSeq.java
changed	/trunk/Source/edu/utah/seq/analysis/BisStatRegionMaker.java
changed	/trunk/Source/edu/utah/seq/analysis/EnrichedRegionMaker.java
changed	/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java
changed	/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java
changed	/trunk/Source/edu/utah/seq/data/Info.java
changed	/trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed	/trunk/Source/edu/utah/seq/data/SamComparator.java
changed	/trunk/Source/edu/utah/seq/data/sam/SamLayout.java
changed	/trunk/Source/edu/utah/seq/data/sam/SamLayoutForMutation.java
changed	/trunk/Source/edu/utah/seq/its/Interval.java
changed	/trunk/Source/edu/utah/seq/its/IntervalTree.java
changed	/trunk/Source/edu/utah/seq/parsers/FilterDuplicateAlignments.java
added	/trunk/Source/edu/utah/seq/parsers/MergePairedAlignments.java
changed	/trunk/Source/edu/utah/seq/parsers/MergePairedSamAlignments.java
changed	/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java
changed	/trunk/Source/edu/utah/seq/parsers/NovoalignIndelParser.java

/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view

/trunk/LibraryJars/poi-3.10.1-20140818.jar

Binary file was added.

/trunk/LibraryJars/poi-ooxml-3.10.1-20140818.jar

Binary file was added.

/trunk/LibraryJars/poi-ooxml-schemas-3.10.1-20140818.jar

Binary file was added.

/trunk/Source/edu/utah/seq/analysis/AggregatePlotter.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/AllelicExpressionComparator.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/AllelicExpressionDetector.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/AllelicExpressionSnp.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/BisSeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/BisStatRegionMaker.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/EnrichedRegionMaker.java Diff Switch to side-by-side view

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

/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view

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

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

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

/trunk/Source/edu/utah/seq/its/Interval.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/its/IntervalTree.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/FilterDuplicateAlignments.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/MergePairedAlignments.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/MergePairedSamAlignments.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/NovoalignIndelParser.java Diff Switch to side-by-side view

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