USeq Source Code

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

Commit [r239] Maximize Restore History

TomatoFarmer Overhaul

1) Works with pysano
2) Code is more organized
3) Can result incomplete jobs
4) Only recalibrates by sample (not by lane)

Authored by: tmosbruger 2014-06-04

Parent: [r238]

Child: [r240]

1 2 > >> (Page 1 of 2)

changed	/trunk/Source/edu/utah/diagnostics/ParseExonMetrics.java
changed	/trunk/Source/edu/utah/seq/parsers/AlignmentEndTrimmer.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFInfo.java
renamed	/trunk/Source/edu/utah/tomato/StringPattern.java -> /trunk/Source/edu/utah/tomato/model/TFMatchObject.java
renamed	/trunk/Source/edu/utah/tomato/TFCommand.java -> /trunk/Source/edu/utah/tomato/model/TFCommand.java
renamed	/trunk/Source/edu/utah/tomato/TFCommandExomeAlign.java -> /trunk/Source/edu/utah/tomato/model/command/TFCommandExomeAlignUgp.java
renamed	/trunk/Source/edu/utah/tomato/TFCommandExomeMetrics.java -> /trunk/Source/edu/utah/tomato/model/command/TFCommandExomeMetrics.java
removed	/trunk/Source/edu/utah/tomato/TFConstants.java
removed	/trunk/Source/edu/utah/tomato/TFLogger.java
renamed	/trunk/Source/edu/utah/tomato/TFSampleInfo.java -> /trunk/Source/edu/utah/tomato/model/TFSampleInfo.java
renamed	/trunk/Source/edu/utah/tomato/TFThread.java -> /trunk/Source/edu/utah/tomato/daemon/TFThread.java
renamed	/trunk/Source/edu/utah/tomato/TFThreadDaemon.java -> /trunk/Source/edu/utah/tomato/daemon/TFThreadDaemon.java
changed	/trunk/Source/edu/utah/tomato/TomatoFarmer.java
added	/trunk/Source/edu/utah/tomato/daemon
added	/trunk/Source/edu/utah/tomato/model
added	/trunk/Source/edu/utah/tomato/model/TFFileObject.java
added	/trunk/Source/edu/utah/tomato/model/command
added	/trunk/Source/edu/utah/tomato/model/command/TFCommandExomeAlignHci.java