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Mods to STP to output just spliced alignments.

Mods to VCFAnnotator to convert scores to pvalues.
Mods to MiRNACorrelator to improve ggplot scripts.

biotelerock 2014-01-04

Browse code at this revision

Parent: [r201]

Child: [r203]

changed /trunk/Source/edu/expr/MiRNACorrelator.java
changed /trunk/Source/edu/utah/seq/data/sam/SamAlignment.java
changed /trunk/Source/edu/utah/seq/parsers/SamTranscriptomeParser.java
renamed /trunk/Source/edu/utah/seq/vcf/VCFSpliceAnnotator.java -> /trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java
added /trunk/Source/edu/utah/seq/vcf/splice
changed /trunk/Source/util/gen/Bin.java
changed /trunk/Source/util/gen/Histogram.java
/trunk/Source/edu/expr/MiRNACorrelator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/sam/SamAlignment.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/parsers/SamTranscriptomeParser.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFSpliceAnnotator.java to /trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java
File was renamed.
/trunk/Source/edu/utah/seq/vcf/splice
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/trunk/Source/util/gen/Bin.java Diff Switch to side-by-side view
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/trunk/Source/util/gen/Histogram.java Diff Switch to side-by-side view
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