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Lots of modifications for calling snp bases in BAM alignments

biotelerock 2012-12-11

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Parent: [r21]

Child: [r23]

changed /trunk/Source/edu/utah/seq/base/Classifier.java
changed /trunk/Source/edu/utah/seq/base/SNPComparator.java
changed /trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java
changed /trunk/Source/edu/utah/seq/base/VariantAlignment.java
/trunk/Source/edu/utah/seq/base/Classifier.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/SNPComparator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/VariantAlignment.java Diff Switch to side-by-side view
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