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Package org.broad.igv.sam.reader

Abstract
abstract class AlignmentIndexer
Interface
interface AlignmentParser
Interface
interface AlignmentReader
class AlignmentReaderFactory
class BAMReader
Created by IntelliJ IDEA. User : jrobinso Date: Sep 22, 2009 Time: 2:21:04 PM
class CGIAlignmentReader
Reader for querying a CGI serv ice for SAM (note not BAM) fi les.
class DotAlignedCodec
private String chromosome; pri vate int start; private int e nd; boolean negativeStrand;
class DotAlignedIndexer
Created by IntelliJ IDEA.
class DotAlignedParser
class FeatureIndex
class GeraldReader
A wrapper for SamTextReader th at supports query by interval .
class IndexLoadException
Created by IntelliJ IDEA. User : jrobinso Date: Nov 2, 2009 Time: 9:45:22 PM To chang...
class IndexNotFoundException
class MergedAlignmentReader
Performs a logical merge of ba m files. User: jrobinso Date: Apr 25, 2010
class PSLAlignmentParser
class ReadGroupFilter
Created by IntelliJ IDEA. User : jrobinso Date: Oct 1, 2009 Time: 7:09:37 PM To chang...
class SAMQueryIterator
class SAMReader
A wrapper for SamTextReader th at supports query by interval .
class SamIndexer
Created by IntelliJ IDEA.
class SamUtils
class SolexaQualityConverter
Optimized method for convertin g Solexa ASCII qualities into Phred scores. Pre-comput...
class UnsortedFileException
class WrappedIterator
Interface
interface CloseableIterator
class? RuntimeException
class? Exception
EMPTY_ITERATORfeatureIndexparserreaders 0..* filterCache 0..* wrappedIteratorfeatureIndexsingletoniter