USeq Source Code

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

Commit [r217] Maximize Restore History

Lots of mods, most are related to changing a method for parsing bed files giving the option to ignore strand.

Authored by: biotelerock 2014-02-06

Browse code at this revision

Parent: [r216]

Child: [r218]

changed	/trunk/Source/edu/expr/MiRNACorrelator.java
changed	/trunk/Source/edu/utah/seq/analysis/AllelicMethylationDetector.java
removed	/trunk/Source/edu/utah/seq/base/SNPComparator.java
changed	/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java
changed	/trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed	/trunk/Source/edu/utah/seq/data/SamSVFilter.java
added	/trunk/Source/edu/utah/seq/data/SamSVJoiner.java
changed	/trunk/Source/edu/utah/seq/data/sam/SamAlignment.java
changed	/trunk/Source/edu/utah/seq/parsers/ParseIntersectingAlignments.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFComparator.java
changed	/trunk/Source/edu/utah/seq/vcf/splice/SpliceHit.java
changed	/trunk/Source/edu/utah/seq/vcf/splice/SpliceJunction.java
changed	/trunk/Source/edu/utah/seq/vcf/splice/VCFSpliceAnnotator.java
changed	/trunk/Source/trans/misc/Bed2Bar.java
changed	/trunk/Source/trans/misc/Bed2Blocks.java
changed	/trunk/Source/util/apps/CompareIntersectingRegions.java
changed	/trunk/Source/util/apps/FindSharedRegions.java
changed	/trunk/Source/util/apps/MergeColumns.java
changed	/trunk/Source/util/bio/annotation/Bed.java
changed	/trunk/Source/util/bio/seq/MaskRegionsInFastaFiles.java
changed	/trunk/Source/util/gen/Gzipper.java
changed	/trunk/Source/util/gen/Misc.java
changed	/trunk/Source/util/gen/Num.java

/trunk/Source/edu/expr/MiRNACorrelator.java Diff Switch to side-by-side view

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

/trunk/Source/edu/utah/seq/base/SNPComparator.java

File was removed.

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

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

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

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

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

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

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

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

/trunk/Source/trans/misc/Bed2Bar.java Diff Switch to side-by-side view

/trunk/Source/trans/misc/Bed2Blocks.java Diff Switch to side-by-side view

/trunk/Source/util/apps/CompareIntersectingRegions.java Diff Switch to side-by-side view

/trunk/Source/util/apps/FindSharedRegions.java Diff Switch to side-by-side view

/trunk/Source/util/apps/MergeColumns.java Diff Switch to side-by-side view

/trunk/Source/util/bio/annotation/Bed.java Diff Switch to side-by-side view

/trunk/Source/util/bio/seq/MaskRegionsInFastaFiles.java Diff Switch to side-by-side view

/trunk/Source/util/gen/Gzipper.java Diff Switch to side-by-side view

/trunk/Source/util/gen/Misc.java Diff Switch to side-by-side view

/trunk/Source/util/gen/Num.java Diff Switch to side-by-side view