Class BM_linkPair

Default constructor.

Initializes a BM_LinkPair instance with the provided set of properties.

Inputs:
 cid1 - unique identifier for contig 1
 cid2 - unique identifier for contig 2

Outputs:
 None

Overrides: object.__init__

Add a link between the two contigs

Inputs:
 r1 - int, == 1 if the read maps to contig 1 in reverse orientation
 r2 - int, == 1 if the read maps to contig 2 in reverse orientation
 pos1 - int, leftmost position of read on contig 1
 pos2 - int, leftmost position of read on contig 2
 bamFile - BM_bamFile instance that describes this link

Outputs:
 None

Advanced string function

used for creating output to links file
calls link.printmore()

Inputs:
 contigNames - { cid : string }, storage for long contig names
 contigLengths - { cid : int }, storage for contig lengths
 bamFileNames - { bamId : string }, storage for long bam file names

Outputs:
 Multi-line string descrtibing all the links between the two contigs

override basic string function

Overrides: object.__str__