BisSNP code

Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller

Brought to you by: dnaase

Commit [r27] Maximize Restore History

BisSNP-0.85.3: add BisSNPCoverageWalker and QuickMethylationLevelWalker for MA plot and coverage check plot in bisulfite-seq

Authored by: dnaase 2013-11-01

Browse code at this revision

Parent: [r26]

changed	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/BisSNP.java
changed	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/BisulfiteSNPGenotypeLikelihoodsCalculationModel.java
changed	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/filters/BisulfiteIncompleteConvReadsFilter.java
changed	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/filters/BisulfiteMismatchReadsFilter.java
added	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/otherwalker/BisSNPCoverageWalker.java
added	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/otherwalker/QuickMethylationLevelWalker.java
changed	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/writer/bedObject.java
changed	/trunk/src/edu/usc/epigenome/uecgatk/bissnp/writer/bedObjectWriterImp.java

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/BisSNP.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/BisulfiteSNPGenotypeLikelihoodsCalculationModel.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/filters/BisulfiteIncompleteConvReadsFilter.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/filters/BisulfiteMismatchReadsFilter.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/otherwalker/BisSNPCoverageWalker.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/otherwalker/QuickMethylationLevelWalker.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/writer/bedObject.java Diff Switch to side-by-side view

/trunk/src/edu/usc/epigenome/uecgatk/bissnp/writer/bedObjectWriterImp.java Diff Switch to side-by-side view