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Added options for stranded analysis to the RNAEditing apps

Mods to the VCFComparator and VCFRecord to deal with odd vcf files
Updated the release notes

biotelerock 2013-04-17

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Source/edu/utah/seq/analysis/DefinedRegionRNAEditing.java
changed /trunk/Source/edu/utah/seq/analysis/RNAEditingScanSeqs.java
changed /trunk/Source/edu/utah/seq/vcf/VCFComparator.java
changed /trunk/Source/edu/utah/seq/vcf/VCFMerger.java
changed /trunk/Source/edu/utah/seq/vcf/VCFRecord.java
/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/DefinedRegionRNAEditing.java 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/vcf/VCFComparator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFMerger.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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