Class ReadSetManager

Default constructor.

Initializes a ReadSet instance with the provided set of properties.

Inputs:
 manager - multiprocessing.Manager() instance owned by the
           BamExtractor use this to make all Queues.
Outputs:
 None

Overrides: object.__init__

Stop all the threads from running

Also stops any looping processes in the ReadSets

Inputs:
 None
Outputs:
 None

Set response queues used to pass ReadSets to the extract threads

Inputs:
 queues - dict { outPrefix : mp.Manager().Queue() }, one for each
          thread that's parsing BAM files for the BAmExtractor
Outputs:
 None

Set the print queue for communcating upwards

Inputs:
 queue - mp.Manager().Queue(), print queue managed by the BamExtractor
Outputs:
 None

Ensure that only one thread at a time has access to a read set

Inputs:
 bid - int, the unique identifier for a BAM file
 gid - int, the unique identifier for a target group
 rpi - enum, describes the type of read (RPI.FIR etc.)
 threadId - string, identifies the thread that is requesting
            the resource.
Outputs:
 The requested read set or None if it is not available

Indicate that a thread is finished with a read set

Inputs:
 bid - int, the unique identifier for a BAM file
 gid - int, the unique identifier for a target group
 rpi - enum, describes the type of read (RPI.FIR etc.)
 threadId - string, identifies the thread that is freeing
            the resource.
Outputs:
 None

Raises:
 InvalidParameterSetException - if the supplied information
                                doesn't make sense

Manage requests by parsing threads to access ReadSets

This process runs on it's own thread and continues until it discovers
a None on the requestQueue or self._threadsAreValid is set to False

Inputs:
 None

Outputs:
 None

Determine all the outFile prefixes needed for extraction.

The RSM manages a collection of output file objects called ReadSets
These are made here and placed into hashes for retrieval later. This
function also populates instance variables self.fnPrefix2ReadSet and
self.outFiles; the two main ways that ReadSets can be accessed.

File names vary wildly depending on the values of flags such as:
mixGroups, mixBams etc. Take care when modifying this code.

Inputs:
 prettyBamFileNames - [ string ] simple versions of the BAM filenames
 groupNames - [ string ] identify contig groups. EX: [bin1, bin2]
 zipped - bool, True if the output should be zipped
 interleaved - bool, True if the output should be interleaved
 mixBams - bool, True if BAM file origin should be ignored
 mixGroups - bool, True if group origin should be ignored
 mixReads - bool, True if (un)paired distinction should be ignored
 headersOnly - bool, True if only headers should be printed
 outFolder - string, folder to write output to
 prefix - string, prefix to apply to all output files

Outputs:
 of_prefixes - { bamId : { groupId : { rpi : outFile prefix } } },
               this hash can be used to get the file name prefix for a
               read set based on BAM file origin, group origin and
               pairing information.