Class Summary |
AbstractBAMFileIndex |
Provides basic, generic capabilities to be used reading BAM index files. |
AbstractSAMHeaderRecord |
Base class for the various concrete records in a SAM header, providing uniform
access to the attributes. |
AlignmentBlock |
Represents the contiguous alignment of a subset of read bases to a reference
sequence. |
BamFileIoUtils |
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BAMIndexer |
Class for both constructing BAM index content and writing it out. |
BAMIndexMetaData |
Metadata about the bam index contained within the bam index. |
BamIndexValidator |
One crisp, informative sentence or noun phrase that explains
the concept modeled by the class. |
BAMRecord |
Wrapper class for binary BAM records. |
BAMRecordCodec |
Class for translating between in-memory and disk representation of BAMRecord. |
Bin |
An individual bin in a BAM file. |
BinList |
Provides a list of all bins which could exist in the BAM file. |
BinningIndexBuilder |
Builder for a BinningIndexContent object. |
BinningIndexContent |
In-memory representation of the binning index for a single reference. |
BinningIndexContent.BinList |
This class is used to encapsulate the list of Bins store in the BAMIndexContent
While it is currently represented as an array, we may decide to change it to an ArrayList or other structure |
Chunk |
A [start,stop) file pointer pairing into the BAM file, stored
as a BAM file index. |
Cigar |
A list of CigarElements, which describes how a read aligns with the reference. |
CigarElement |
One component of a cigar string. |
CoordinateSortedPairInfoMap<KEY,REC> |
Holds info about a mate pair for use when processing a coordinate sorted file. |
CRAMFileReader |
BAMFileReader analogue for CRAM files. |
CRAMFileWriter |
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CRAMIndexer |
Class for both constructing BAM index content and writing it out. |
CRAMIterator |
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CRAMIterator.CramFileIterable |
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CustomReaderFactory |
Factory for creating custom readers for accessing API based resources,
e.g. |
Defaults |
Embodies defaults for global values that affect how the SAM JDK operates. |
DefaultSAMRecordFactory |
Default factory for creating SAM and BAM records used by the SAMFileReader classes. |
DuplicateScoringStrategy |
This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
during duplicate marking (see MarkDuplicates). |
FixBAMFile |
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GenomicIndexUtil |
Constants and methods used by BAM and Tribble indices |
LinearIndex |
The linear index associated with a given reference in a BAM index. |
MergingSamRecordIterator |
Provides an iterator interface for merging multiple underlying iterators into a single
iterable stream. |
NotPrimarySkippingIterator |
Wrapper around SAMRecord iterator that skips over non-primary elements. |
QueryInterval |
Interval relative to a reference, for querying a BAM file. |
ReservedTagConstants |
Constants for tags used in our SAM/BAM files |
SAMBinaryTagAndUnsignedArrayValue |
Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because
signedness cannot be determined by introspection of value. |
SAMBinaryTagAndValue |
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute. |
SAMFileHeader |
Header information from a SAM or BAM file. |
SamFileHeaderMerger |
Merges SAMFileHeaders that have the same sequences into a single merged header
object while providing read group translation for cases where read groups
clash across input headers. |
SAMFileReader |
Deprecated. |
SAMFileReader.ReaderImplementation |
Internal interface for SAM/BAM file reader implementations. |
SamFiles |
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SAMFileSource |
Represents the origin of a SAM record. |
SAMFileTruncatedReader |
Deprecated. |
SamFileValidator |
Validates SAM files as follows:
checks sam file header for sequence dictionary
checks sam file header for read groups
for each sam record
reports error detected by SAMRecord.isValid()
validates NM (nucleotide differences) exists and matches reality
validates mate fields agree with data in the mate record
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SamFileValidator.ValidationMetrics |
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SAMFileWriterFactory |
Create a SAMFileWriter for writing SAM or BAM. |
SAMFileWriterImpl |
Base class for implementing SAM writer with any underlying format. |
SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord> |
Provides ordering based on SAM header records' attribute values. |
SamInputResource |
Describes a SAM-like resource, including its data (where the records are), and optionally an index. |
SAMLineParser |
this class enables creation of a SAMRecord object from a String in SAM text format. |
SamPairUtil |
Utility methods for pairs of SAMRecords |
SamPairUtil.SetMateInfoIterator |
A class to iterate through SAMRecords and set mate information on the given records, and optionally
set the mate cigar tag (true by default). |
SAMProgramRecord |
In-memory representation of @PG SAM header record. |
SamReader.AssertingIterator |
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SamReader.PrimitiveSamReaderToSamReaderAdapter |
Decorator for a SamReader.PrimitiveSamReader that expands its functionality into a SamReader . |
SamReader.Type |
Describes a type of SAM file. |
SamReaderFactory |
Describes the functionality for producing SamReader , and offers a
handful of static generators. |
SAMReadGroupRecord |
Header information about a read group. |
SAMRecord |
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SAMRecord.SAMTagAndValue |
Tag name and value of an attribute, for getAttributes() method. |
SAMRecordCoordinateComparator |
Comparator for sorting SAMRecords by coordinate. |
SAMRecordQueryNameComparator |
Comparator for "queryname" ordering of SAMRecords. |
SAMRecordSetBuilder |
Factory class for creating SAMRecords for testing purposes. |
SAMRecordUtil |
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SAMSequenceDictionary |
Collection of SAMSequenceRecords. |
SAMSequenceRecord |
Header information about a reference sequence. |
SAMSortOrderChecker |
Encapsulates simple check for SAMRecord order. |
SamStreams |
Utilities related to processing of InputStream s encoding SAM data |
SAMTagUtil |
Facility for converting between String and short representation of a SAM tag. |
SAMTestUtil |
Misc methods for SAM-related unit tests. |
SAMTextHeaderCodec |
Parser for a SAM text header, and a generator of SAM text header. |
SAMTextWriter |
Writer for text-format SAM files. |
SAMTools |
Command line utility for manipulating SAM/BAM files. |
SAMUtils |
Utilty methods. |
SAMValidationError |
Class that encapsulates a validation error message as well as a type code so that
errors can be aggregated by type. |
SecondaryOrSupplementarySkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary and supplementary elements. |
SQTagUtil |
Utility methods for encoding and decoding the SQ tag value of SAMRecord. |
TagValueAndUnsignedArrayFlag |
CVO to use as a method return value. |
TextCigarCodec |
Convert between String and Cigar class representations of CIGAR. |
TextTagCodec |
Converter between SAM text representation of a tag, and in-memory Object representation. |