Class BamParser

Default constructor.

Set quality thresholds used in later parsing

Inputs:
 coverageType - BM_coverageType, stores type of coverage to calculate
 minLength - int, ignore contigs shorter than this length
 mappingQuality - int, ignore positions with a lower base quality score
 mappingQuality - int, skip all reads with a lower mapping quality score
 useSuppAlignments - == True -> DON'T skip supplementary alignments
 useSecondaryAlignments - == True -> DON'T skip secondary alignments
 maxMisMatches - int, skip all reads with more mismatches (NM aux files)

Outputs:
 None

Parse bam files to get coverage and linking reads.

Manages threading
Stores results in internal mapping results list

Inputs:
 bamFiles - [string], full paths to BAMs
 doLinks - == True -> find linking pairs
 doCovs - == True -> calculate coverage profiles
 types - [int] or None, number of insert types per bamfile
 threads - int, max number of threads to use
 verbose - == True -> be verbose

Outputs:
 0 if the parsing worked, 1 otherwise

Collapse multiple BFI objects into one and
set it as member variable BFI

Only one of the threads will bother to parse contig names. Find it's
BFI and then merge all the other BFIs (from other threads) into it

Inputs:
 BFI_list - Manager.List, list of all BFIs created during parsing

Outputs:
 None

Print template size and orientation information
to a file or to stdout.

Inputs:
 fileName - string, full path to output file or ""

Outputs:
 None

Print coverage profile information to a file or to stdout

Inputs:
 fileName - string, full path to output file or ""

Outputs:
 None

Print paired links information to a file or to stdout

Inputs:
 fileName - string, full path to output file or ""

Outputs:
 None