USeq Source Code

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

Commit [r281] Maximize Restore History

AllelicExpressionDetector - cleaned up code

SamAlignmentExtractor - removed option on printing coverage stats, now directing to a file instead of stdout
MultiSampleVCFFilter - fixed issue with gzipped vcfs and not tabix provided
SomaticSniperVCFParser - new app for inserting quality score into QUAL field and option for score filtering
VCFComparator - more mods to support bed file key variants

Authored by: biotelerock 2015-01-08

Browse code at this revision

Parent: [r280]

Child: [r282]

changed	/trunk/Source/edu/utah/seq/analysis/AllelicExpressionDetector.java
changed	/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java
changed	/trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java
added	/trunk/Source/edu/utah/seq/vcf/SomaticSniperVCFParser.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFComparator.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFSample.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFUtilities.java
changed	/trunk/build.properties

USeq Source Code

Commit [r281] Maximize Restore History

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

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

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

/trunk/build.properties Diff Switch to side-by-side view