Class BamScheduler

Default constructor.

Initializes a BamScheduler instance with the provided set of properties.

Inputs:
 database - full path to fasta file of contigs (may be gzipped),
 alignmentAlgorithm - one of BWA's alignment algorithms,
 indexAlgorithm - one of BWA's index algorithms,
 paired - [fileName pairs], always even numbered in length, in order
          [R_A_1, R_A_2, R_B_1, R_B_2, ...]
 interleaved - [fileNames], containing interleaved paired reads
 singleEnded - [fileNames], containing single ended reads
 keptFiles - == True -> indexes for the db already exist,
 keepFiles - == True -> don't delete indexes at the end,
 outputTam - == True -> you love text files to bits,
 numThreads - int, the maximum number of threads to use
 maxMemory - string, maximum memory program will use (samtools style)
 forceOverwriting - == True -> force overwriting index files,
 extraArguments - string, extra args to pass to BWA
 showCommands - == True -> show all commands being run
 quiet - == True -> suppress output from the mapper
 silent - == True -> suppress all output

Outputs:
 None

sequentially make the bam files

Inputs:
 None

Outputs:
 None

Consistent way to make output file name prefixes

Inputs:
 readsFile - path-free read file name

Outputs:
 pretty prefix

Make sure that a path exists, make it if necessary

Inputs:
 path - string, full or relative path to create

Outputs:
 None