USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Commit [r238] Maximize Restore History

Updated picard jars. They did a big package rearrangement so had to modify a bunch of classes. Might be a bit painful to get stuff fixed.

Authored by: biotelerock 2014-05-28

Browse code at this revision

Parent: [r237]

Child: [r239]

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changed	/trunk/Source/edu/utah/seq/data/SamSVJoiner.java
changed	/trunk/Source/edu/utah/seq/data/SamSubsampler.java
changed	/trunk/Source/edu/utah/seq/data/sam/ClusterDataToSamConverter.java
changed	/trunk/Source/edu/utah/seq/data/sam/ExampleSamUsage.java
changed	/trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsConverter.java
changed	/trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsToSam.java
changed	/trunk/Source/edu/utah/seq/data/sam/IlluminaBasecallsToSamConverter.java
changed	/trunk/Source/edu/utah/seq/data/sam/PicardSortSam.java
added	/trunk/Source/edu/utah/seq/its
added	/trunk/Source/edu/utah/seq/its/Interval.java
added	/trunk/Source/edu/utah/seq/its/IntervalTree.java
added	/trunk/Source/edu/utah/seq/its/LeftComparator.java
added	/trunk/Source/edu/utah/seq/its/Node.java
added	/trunk/Source/edu/utah/seq/its/RightComparator.java
added	/trunk/Source/edu/utah/seq/its/SamIntervalTree.java
added	/trunk/Source/edu/utah/seq/its/TestIntervalTree.java
changed	/trunk/Source/edu/utah/seq/parsers/AlignmentEndTrimmer.java
changed	/trunk/Source/edu/utah/seq/parsers/MergePairedSamAlignments.java
changed	/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java
changed	/trunk/Source/edu/utah/seq/parsers/ParsedAlignment.java
changed	/trunk/Source/edu/utah/seq/parsers/Sam2Fastq.java
changed	/trunk/Source/edu/utah/seq/parsers/SamParser.java
changed	/trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java
changed	/trunk/Source/edu/utah/tomato/TFCommandExomeVariant.java
changed	/trunk/Source/util/bio/parsers/UCSCGeneLine.java