| Generated and automatically maintained for github.com/igvteam/igv by SourceSpy
GitHub Project BadgeCopy: HTML Markdown

Package org.broad.igv.sam.reader

org.broad.igv.sam.reader
Abstract
AlignmentIndexer
Interface
AlignmentParser
Interface
AlignmentReader
AlignmentReaderFactory
BAMReader
Created by IntelliJ IDEA. User : jrobinso Date: Sep 22, 2009 Time: 2:21:04 PM
CGIAlignmentReader
Reader for querying a CGI serv ice for SAM (note not BAM) fi les.
DotAlignedCodec
private String chromosome; pri vate int start; private int e nd; boolean negativeStrand;
Interface
SortingCollection.Codec
Client must implement this cla ss, which defines the way in which records are written...
Interface
Cloneable
DotAlignedIndexer
Created by IntelliJ IDEA.
DotAlignedParser
FeatureIndex
GeraldReader
A wrapper for SamTextReader th at supports query by interval .
IndexLoadException
Created by IntelliJ IDEA. User : jrobinso Date: Nov 2, 2009 Time: 9:45:22 PM To chang...
Exception
IndexNotFoundException
RuntimeException
JProgressBar
MergedAlignmentReader
Performs a logical merge of ba m files. User: jrobinso Date: Apr 25, 2010
PSLAlignmentParser
ReadGroupFilter
Created by IntelliJ IDEA. User : jrobinso Date: Oct 1, 2009 Time: 7:09:37 PM To chang...
SAMQueryIterator
Interface
CloseableIterator
SAMReader
A wrapper for SamTextReader th at supports query by interval .
SAMTextHeaderCodec
SamIndexer
Created by IntelliJ IDEA.
SamInputResource
SamUtils
SolexaQualityConverter
Optimized method for convertin g Solexa ASCII qualities into Phred scores. Pre-comput...
UnsortedFileException
WrappedIterator