Class to hold Paired reads.

Holds the reference sequence information.

Class to hold Reads or aligned sequence or query sequence in SAM Alignment.

SAMAlignedSequenceHeader holds aligned sequence headers of the sam file format.

Class to hold SAM Headers.

SAM Dna Alphabet, Supports "=ACMGRSVTWYHKDBN." symbols.

Writes a SequenceAlignmentMap to a particular location, usually a file. The output is formatted according to the SAM file format specification 1.4. A method is also provided for quickly accessing the content in string form for applications that do not need to first write to file. Documentation for the latest SAM file format can be found at http://samtools.sourceforge.net/SAM1.pdf

This class holds SAM optional field.

A SAMParser reads from a source of text that is formatted according to the SAM file specification (v1.4-r985), and converts the data to in-memory SequenceAlignmentMap object. For advanced users, the ability to select an encoding for the internal memory representation is provided. There is also a default encoding for each alphabet that may be encountered. Documentation for the latest SAM file format can be found at http://samtools.sourceforge.net/SAM1.pdf

This class holds SAM record fields. Record fields are present in the SAM header. This class can hold one header line of the SAM header. For example, consider the following header line. @SQ SN:chr20 LN:62435964 In this example SQ is the Type code. SN:chr20 and LN:62435964 are SAMRecordFieldTags.

This class holds the tag in the header lines. For example, consider the following header line. @HD VN:1.0 In this example VN:1.0 is the SAMRecordFieldTag. Where VN is stored in Tag property and 1.0 is stored in the value property of this class.

Class to hold sequence alignment map (SAM) structure.

Specifies the type of paired read.

SAM Flags. This enum represents the bitwise flags of the SAM format.