USeq Source Code

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

Commit [r299] Maximize Restore History

Whole lot of mods and apps related to Bam QC, Extracting alignments, and calling CNVs. New app for injecting variants from a VCF file into bam alignments. Gave up fighting with BamSurgeon.

Authored by: biotelerock 2015-06-19

Browse code at this revision

Parent: [r298]

Child: [r300]

changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed	/trunk/Source/edu/utah/seq/cnv/PoReCNV.java
changed	/trunk/Source/edu/utah/seq/data/CalculatePerCycleErrorRate.java
changed	/trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed	/trunk/Source/edu/utah/seq/data/SamSplitter.java
changed	/trunk/Source/edu/utah/seq/data/SamSubsampler.java
added	/trunk/Source/edu/utah/seq/data/sam/SamLayoutLite.java
changed	/trunk/Source/edu/utah/seq/parsers/MergePairedAlignments.java
changed	/trunk/Source/edu/utah/seq/parsers/SamAlignmentExtractor.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFRecord.java
added	/trunk/Source/edu/utah/seq/vcf/sim/BamBlaster.java
changed	/trunk/Source/edu/utah/seq/vcf/sim/BamSurgeonMutator.java
changed	/trunk/Source/util/bio/seq/Seq.java
changed	/trunk/Source/util/gen/Misc.java
changed	/trunk/build.properties
changed	/trunk/build.xml

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

/trunk/Source/edu/utah/seq/cnv/PoReCNV.java Diff Switch to side-by-side view

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

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

USeq Source Code

Commit [r299] Maximize Restore History

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

/trunk/Source/edu/utah/seq/cnv/PoReCNV.java Diff Switch to side-by-side view

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

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

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

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

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

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

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

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

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

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