USeq Source Code

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

Commit [r32] Maximize Restore History

Lots of modifications for making merged sam alignments from proper pairs.

Many changes to the base recalling applications.

Authored by: biotelerock 2012-12-15

Browse code at this revision

Parent: [r31]

Child: [r33]

changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed	/trunk/Source/edu/utah/seq/base/BaseClassifier.java
changed	/trunk/Source/edu/utah/seq/base/SNPComparator.java
removed	/trunk/Source/edu/utah/seq/base/VCFParser.java
changed	/trunk/Source/edu/utah/seq/data/sam/SamAlignment.java
changed	/trunk/Source/edu/utah/seq/data/sam/SamAlignmentFlags.java
added	/trunk/Source/edu/utah/seq/data/sam/SamLayout.java
changed	/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java
changed	/trunk/Source/edu/utah/seq/parsers/Sam2Fastq.java
changed	/trunk/Source/edu/utah/seq/parsers/SamFixer.java
changed	/trunk/Source/edu/utah/seq/parsers/SamParser.java
changed	/trunk/Source/edu/utah/seq/parsers/SamTranscriptomeParser.java
changed	/trunk/Source/edu/utah/seq/parsers/VCFRecord.java
changed	/trunk/Source/util/bio/seq/Seq.java
changed	/trunk/Source/util/gen/Misc.java

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

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

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

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

File was removed.

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

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

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

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

/trunk/Source/edu/utah/seq/parsers/Sam2Fastq.java Diff Switch to side-by-side view

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

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

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

/trunk/Source/edu/utah/seq/parsers/VCFRecord.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