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Commit [r273]  Maximize  Restore  History

Lots of mods related to splice site identification in VCF files, improvements to our bam file QC apps, and extended functionality for comparing VCF files with a relaxed key of BamSurgeon induced variants.

biotelerock 2014-12-04

changed /trunk/Documentation/USeqDocumentation/applications.html
changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java
changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed /trunk/Source/edu/utah/seq/parsers/MergePairedAlignments.java
changed /trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java
changed /trunk/Source/edu/utah/seq/vcf/VCFComparator.java
changed /trunk/Source/edu/utah/seq/vcf/VCFSample.java
changed /trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java
changed /trunk/build.properties
/trunk/Documentation/USeqDocumentation/applications.html Diff Switch to side-by-side view
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/trunk/Documentation/USeqDocumentation/releaseNotes.txt 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/parsers/MergePairedAlignments.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/VCFComparator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFSample.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java Diff Switch to side-by-side view
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/trunk/build.properties Diff Switch to side-by-side view
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