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New apps imported from Picard and modified for extracting intenstiy info from CIF files

biotelerock 2013-06-20

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Parent: [r122]

Child: [r124]

added /trunk/Source/edu/utah/seq/data/sam/ClusterDataToSamConverter.java
added /trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsConverter.java
changed /trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsToSam.java
/trunk/Source/edu/utah/seq/data/sam/ClusterDataToSamConverter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsConverter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsToSam.java Diff Switch to side-by-side view
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