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DefinedRegionDifferentialSeq

* Fixed bug when DESeq was outputting FDRs with "NA", these were being assigned the max FDR, switched it to 0.
Note, this won't effect most analysis since these genes also have a log2 of 0 and wouldn't survive standard log2Ratio thresholding.

NovoalignBisulfiteParser
* Fixed a bug in the -b4 novoalignment parsing
* Remove support for native novoalign format, just sam/ bam now.

biotelerock 2013-11-27

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Documentation/USeqDocumentation/usageBisSeq.html
changed /trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java
changed /trunk/Source/edu/utah/seq/analysis/multi/PairedCondition.java
changed /trunk/Source/edu/utah/seq/data/ParsePointDataContexts.java
changed /trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java
changed /trunk/build.properties
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/trunk/Documentation/USeqDocumentation/usageBisSeq.html Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/analysis/multi/PairedCondition.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/ParsePointDataContexts.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.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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