USeq Source Code

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

Commit [r113] Maximize Restore History

Lots of mods to support more efficient loading of vcf files for the VCFComparator. New app for scanning defined regions of methylation array data.

Authored by: biotelerock 2013-05-16

Browse code at this revision

Parent: [r112]

Child: [r114]

changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed	/trunk/Source/edu/utah/seq/analysis/DefinedRegionBisSeq.java
added	/trunk/Source/edu/utah/seq/analysis/MethylationArrayDefinedRegionScanner.java
renamed	/trunk/Source/edu/utah/seq/analysis/MethylationArrayScanSeqs.java -> /trunk/Source/edu/utah/seq/analysis/MethylationArrayScanner.java
changed	/trunk/Source/edu/utah/seq/data/Sam2USeq.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/vcf/MultiSampleVCFFilter.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFComparator.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFMerger.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFParser.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFRecord.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFReporter.java

/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/DefinedRegionBisSeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MethylationArrayDefinedRegionScanner.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MethylationArrayScanSeqs.java to /trunk/Source/edu/utah/seq/analysis/MethylationArrayScanner.java

File was renamed.

/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/ParsedAlignment.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFComparator.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFMerger.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFRecord.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFReporter.java Diff Switch to side-by-side view