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Added some new classes, updates to Autoaligner (new sequencing application codes).

monkeymanstan 2014-06-13

added /trunk/Source/edu/utah/ames/bioinfo/AmesUtil.java
changed /trunk/Source/edu/utah/ames/bioinfo/Autoaligner.java
added /trunk/Source/edu/utah/ames/bioinfo/ExpressionCorrelation.java
added /trunk/Source/edu/utah/ames/bioinfo/FastqFile.java
added /trunk/Source/edu/utah/ames/bioinfo/FileHead.java
added /trunk/Source/edu/utah/ames/bioinfo/Gene.java
changed /trunk/Source/edu/utah/ames/bioinfo/Ketchup.java
added /trunk/Source/edu/utah/ames/bioinfo/Logger.java
added /trunk/Source/edu/utah/ames/bioinfo/MakeXlsxWorkbook.java
added /trunk/Source/edu/utah/ames/bioinfo/MathStuff.java
added /trunk/Source/edu/utah/ames/bioinfo/MeasureContaminatingSeqs.java
added /trunk/Source/edu/utah/ames/bioinfo/Read.java
added /trunk/Source/edu/utah/ames/bioinfo/RegexTest.java
added /trunk/Source/edu/utah/ames/bioinfo/Region.java
changed /trunk/Source/edu/utah/ames/bioinfo/ScratchMasher.java
added /trunk/Source/edu/utah/ames/bioinfo/SequencingApplicationCodeEnumerator.java
added /trunk/Source/edu/utah/ames/bioinfo/StaggeredJobStarter.java
added /trunk/Source/edu/utah/ames/bioinfo/StreamGobbler.java
/trunk/Source/edu/utah/ames/bioinfo/AmesUtil.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Autoaligner.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/ExpressionCorrelation.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/FastqFile.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/FileHead.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Gene.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Ketchup.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Logger.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/MakeXlsxWorkbook.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/MathStuff.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/MeasureContaminatingSeqs.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Read.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/RegexTest.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/Region.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/ScratchMasher.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/SequencingApplicationCodeEnumerator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/StaggeredJobStarter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/ames/bioinfo/StreamGobbler.java Diff Switch to side-by-side view
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