Writes a SequenceAlignmentMap to a particular location, usually a file. The output is formatted according to the BAM file format. Documentation for the latest BAM file format can be found at http://samtools.sourceforge.net/SAM1.pdf

Class to hold BAMIndex information.

Class to read or write BAMIndex data from a file or a stream.

A BAMParser reads from a source of binary data that is formatted according to the BAM file specification, and converts the data to in-memory SequenceAlignmentMap object. Documentation for the latest BAM file format can be found at http://samtools.sourceforge.net/SAM1.pdf

Class to hold BAM file index information related to a reference sequence. Holds bin and linear index information for a reference sequence.

Class to hold Bin information. An instance of this class can contain Bin number and list of chunks related to the bin number.

Class to hold start and end offsets of a BAM file chunk related to a bin.

Singleton Class to Sort Chunks to help merging of chunks.

A list of strings where each item in the list has been validated to meet the conditions of a particular regular expression, used to verify that any item retrieved from this list follows the condition given.

Class to hold offset of a BAM file.

Defines list of possible sort option for SequenceAlignmentMap