Class Hierarchy

bamm.bamExtractor.BamExtractor: Class used to manage extracting reads from multiple BAM files
bamm.bamMaker.BamMaker: Class that wraps bwa and samtools.
bamm.bamParser.BamParser: class for generating coverage profiles and linking read information from several BAM files
bamm.bamMaker.BamScheduler: Class for scheduling making multiple BAM and TAM files
bamm.cWrapper.CWrapper: Multiprocessing can't pickle cTypes pointers and functions.
object: The most base type
- bamm.bamFile.BM_bamFile: Container class for storing information about a BAM file
- bamm.bamFile.BM_bamType: Container class for Storing information about the inserts and orientation types of a BAM file
- bamm.bamFile.BM_coverageType: Container class for storing the type of coverage to calculate
- bamm.bamFile.BM_fileInfo: High level management of BamFiles, contigs and associated mapping statistics
- bamm.bamLink.BM_linkInfo: A single link joining two contigs
- bamm.bamLink.BM_linkPair: Container class for storing all links joining two contigs
- exceptions.BaseException: Common base class for all exceptions
  - bamm.bammExceptions.BamMException
  - bamm.bammExceptions.InvalidParameterSetException
- bamm.cWrapper.CT
- bamm.cWrapper.MI
- bamm.cWrapper.OT
- bamm.cWrapper.RPI
- bamm.bamRead.ReadSet: Container class to encapsulate the concept of a(n un)paired read set
- bamm.bamRead.ReadSetManager: The principle manager of a collection of ReadSet objects
- unreachable._CData: XXX to be provided
  - _ctypes.Structure: Structure base class
    - bamm.cWrapper.BM_LinkWalker_C: typedef struct {...
    - bamm.cWrapper.BM_bamFile_C: typedef struct BM_bamFile {...
    - bamm.cWrapper.BM_bamType_C: typedef struct BM_bamType {...
    - bamm.cWrapper.BM_coverageType_C: typedef struct BM_coverageType {...
    - bamm.cWrapper.BM_fileInfo_C: typedef struct BM_fileInfo {...
    - bamm.cWrapper.BM_linkInfo_C: typedef struct {...
    - bamm.cWrapper.BM_linkPair_C: typedef struct {...
    - bamm.cWrapper.BM_mappedRead_C: typedef struct BM_mappedRead {...
    - bamm.cWrapper.cfuhash_table_t