USeq Source Code

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

Commit [r182] Maximize Restore History

Updates to bisulfite processing to support -b4 novoalignments, reinstatement of overlapping paired read collapsing, additions to VCF classes to allow for scoring splice junction effects.

Authored by: biotelerock 2013-11-20

Browse code at this revision

Parent: [r181]

Child: [r183]

changed	/trunk/Source/edu/utah/seq/data/sam/SamAlignment.java
changed	/trunk/Source/edu/utah/seq/mes/MaxEntScanScore3.java
changed	/trunk/Source/edu/utah/seq/mes/MaxEntScanScore5.java
changed	/trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java
changed	/trunk/Source/edu/utah/seq/parsers/ParsedAlignment.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFParser.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFRecord.java
changed	/trunk/Source/util/bio/annotation/ExonIntron.java

USeq Source Code

Commit [r182] Maximize Restore History

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

/trunk/Source/edu/utah/seq/mes/MaxEntScanScore3.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/mes/MaxEntScanScore5.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/ParsedAlignment.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFParser.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/util/bio/annotation/ExonIntron.java Diff Switch to side-by-side view