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New app CalculatePerCycleErrorRate, mod to MergePairedSamAlignments to skip merging phiX, new methods to Num, updated releaseNotes and the build.properties.

biotelerock 2013-01-11

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Source/edu/utah/seq/analysis/RNAEditingScanSeqs.java
added /trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java
changed /trunk/Source/edu/utah/seq/parsers/MergePairedSamAlignments.java
changed /trunk/Source/util/gen/Num.java
changed /trunk/build.properties
/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/RNAEditingScanSeqs.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/parsers/MergePairedSamAlignments.java Diff Switch to side-by-side view
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/trunk/Source/util/gen/Num.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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