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SamTranscriptomeParser & DefinedRegionDifferentialSeq

* Replaced the IH tag with NH tag for reporting the number of alignments present per read to be compatible with DEXSeq's HTSeq app.

SamReadDepthSubSampler
* New app for reducing extreme read depths in amplicon based sequencing datasets

More mods to the SpliceJunction annotator for zscore estimations

biotelerock 2014-02-18

changed /trunk/Source/edu/utah/seq/analysis/BisStat.java
changed /trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java
changed /trunk/Source/edu/utah/seq/base/NMer.java
changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
added /trunk/Source/edu/utah/seq/data/SamReadDepthSubSampler.java
added /trunk/Source/edu/utah/seq/data/sam/ComparatorSamAlignmentName.java
changed /trunk/Source/edu/utah/seq/data/sam/SamAlignment.java
changed /trunk/Source/edu/utah/seq/mes/MaxEntScanScore3.java
changed /trunk/Source/edu/utah/seq/mes/MaxEntScanScore5.java
changed /trunk/Source/edu/utah/seq/parsers/SamTranscriptomeParser.java
changed /trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java
changed /trunk/Source/util/gen/Histogram.java
changed /trunk/Source/util/gen/StandardDeviation.java
changed /trunk/build.properties
changed /trunk/build.xml
/trunk/Source/edu/utah/seq/analysis/BisStat.java 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/base/NMer.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/data/SamReadDepthSubSampler.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/sam/ComparatorSamAlignmentName.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/mes/MaxEntScanScore3.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/mes/MaxEntScanScore5.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/splice/VCFSpliceAnnotator.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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/trunk/Source/util/gen/StandardDeviation.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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/trunk/build.xml Diff Switch to side-by-side view
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