Package htsjdk.samtools
package htsjdk.samtools
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ClassDescriptionProvides basic, generic capabilities to be used reading BAM index files.Base class for the various concrete records in a SAM header, providing uniform access to the attributes.Represents the contiguous alignment of a subset of read bases to a reference sequence.Class for reading and querying BAM files.An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file.Concrete implementation of SAMFileWriter for writing gzipped BAM files.A basic interface for querying BAM indices.Class for both constructing BAM index content and writing it out.Merges BAM index files for (headerless) parts of a BAM file into a single index file.Metadata about the bam index contained within the bam index.Class to validate (at two different levels of thoroughness) the index for a BAM file.Filters out records that do not match any of the given intervals and query type.Wrapper class for binary BAM records.Class for translating between in-memory and disk representation of BAMRecord.Writes SBI files for BAM files, as understood by
SBIIndex.A decorating iterator that filters out records that do not match the given reference and start position.Class for writing SAMRecords in BAM format to an output stream.An individual bin in a BAM file.Converter between disk and in-memory representation of a SAMRecord tag.Provides a list of all bins which could exist in the BAM file.Builder for a BinningIndexContent object.coordinates are 1-based, inclusiveIn-memory representation of the binning index for a single reference.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 structureAn individual bin of a CSI index for BAM files.An index interface with additional functionality for querying and inspecting the structure of a BAM index.A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index.A list of CigarElements, which describes how a read aligns with the reference.One component of a cigar string.The operators that can appear in a cigar string, and information about their disk representations.CoordinateSortedPairInfoMap<KEY,REC> Holds info about a mate pair for use when processing a coordinate sorted file.CoordinateSortedPairInfoMap.Codec<KEY,REC> Client must implement this class, which defines the way in which records are written to and read from file.Class for both constructing BAM index content and writing it out.Class for writing SAMRecords into a series of CRAM containers on an output stream, with an optional index.Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream.BAMFileReaderanalogue for CRAM files.Interface for indexing CRAM.Implementation of the CSI index for BAM files.Factory for creating custom readers for accessing API based resources, e.g.Interface to be implemented by custom factory classes that register themselves with this factory and are loaded dynamically.Embodies defaults for global values that affect how the SAM JDK operates.Default factory for creating SAM and BAM records used by theSamReaderclasses.A class for reading BAM file indices, hitting the disk once per query.Abstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded.A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria.Describes the available downsampling strategies.This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates).Stores a set of records that are duplicates of each other.An iterator of sets of duplicates.Thrown when it is possible to detect that a SAM or BAM file is truncated.Constants and methods used by BAM and Tribble indicesClass for reading and querying BAM files from an htsget sourceFilters out records that do not match any of the given intervals and query type.IndexMerger<T>Merges index files for (headerless) parts of a partitioned main file into a single index file.The linear index associated with a given reference in a BAM index.Provides an iterator interface for merging multiple underlying iterators into a single iterable stream.Deprecated.Interval relative to a reference, for querying a BAM file.Constants for tags used in our SAM/BAM filesSimple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because signedness cannot be determined by introspection of value.Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.Header information from a SAM or BAM file.Little class to generate program group IDsWays in which a SAM or BAM may be sorted.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.Represents the origin of a SAM record.A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query.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 recordInterface for SAMText and BAM file writers.Create a writer for writing SAM, BAM, or CRAM files.Base class for implementing SAM writer with any underlying format.SAM flags as enum, to be used in GUI, menu, etc...This determines how flag fields are represented in the SAM file.Thrown when a SAM file being read or decoded (text or binary) looks bad.SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord>Provides ordering based on SAM header records' attribute values.A helper class to read BAI and CRAI indexes.Describes a SAM-like resource, including its data (where the records are), and optionally an index.This class enables creation of a SAMRecord object from a String in SAM text format.Utility methods for pairs of SAMRecordsThe possible orientations of paired reads.A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default).In-memory representation of @PG SAM header record.Describes functionality for objects that produceSAMRecords and associated information.Facet for index-related operations.The minimal subset of functionality needed for aSAMRecorddata source.Decorator for aSamReader.PrimitiveSamReaderthat expands its functionality into aSamReader, given the backingSamInputResource.Internal interface for SAM/BAM/CRAM file reader implementations, as distinct from non-file-based readers.Describes a type of SAM file.Describes the functionality for producingSamReader, and offers a handful of static generators.A collection of binarySamReaderFactoryoptions.Header information about a read group.Java binding for a SAM file record.Tag name and value of an attribute, for getAttributes() method.Interface for comparators that define the various SAM sort orders.Comparator for sorting SAMRecords by coordinate.Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).Factory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files.A general interface that adds functionality to a CloseableIterator of SAMRecords.SAMRecord comparator that provides an ordering based on a hash of the queryname.Comparator for "queryname" ordering of SAMRecords.Factory class for creating SAMRecords for testing purposes.Collection of SAMSequenceRecords."On the fly" codec SAMSequenceDictionaryCodec.Header information about a reference sequence.Encapsulates simple check for SAMRecord order.Utilities related to processing ofInputStreams encoding SAM dataThe standard tags for a SAM record that are defined in the SAM spec.Deprecated.as of 11/2018, the functions in this class have been absorbed by theSAMTagenum.Misc methods for SAM-related unit tests.Indicates that a required sanity-check condition was not met.Parser for a SAM text header, and a generator of SAM text header.Writer for text-format SAM files.Utilty methods.Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type.SBI is an index into BGZF-compressed data files, which has an entry for the file position of the start of every nth record.Merges SBI files for parts of a file that have been concatenated.Writes SBI files as understood bySBIIndex.Wrapper around SAMRecord iterator that skips over secondary elements.Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.Deprecated.since 11/2018.The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.Emulates BAM index so that we can request chunks of records from SRAFileReader Here is how it works: SRA allows reading of alignments by Reference position fast, so we divide our "file" range for alignments as a length of all references.SRA iterator which returns SAMRecords for requested list of chunksDescribes record ranges info needed for emulating BAM indexCVO to use as a method return value.Convert between String and Cigar class representations of CIGAR.Converter between SAM text representation of a tag, and in-memory Object representation.How strict to be when reading a SAM or BAM, beyond bare minimum validation.
SecondaryAlignmentSkippingIteratorinstead.