Class BamMaker

Default constructor.

Initializes a BamMaker 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,
 outFileName - string, what to name the BAM
 readFile1 - string, full path to 1st read file
 readFile2 - string, full path to 2nd read file or None
 interleaved - == True -> readFile1 is interleaved pairs
 singleEnded - == True -> readFile1 is 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

call BWA make index command

Inputs:
 None

Outputs:
 None

'Remove any index files that are no longer needed

Inputs:
 None

Outputs:
 None

Use BWA ans samtools to make a BAM/TAM file

Inputs:
 None

Outputs:
 None

call bwa aln

Inputs:
 readFile - full path to reads file
 saiFile - full path to corresponding sai file

Outputs:
 None

call bwa sampe

Inputs:
 None

Outputs:
 None

call bwa samse

Inputs:
 None

Outputs:
 None

call bwa sampe and sort + index the result

Inputs:
 None

Outputs:
 None

call bwa samse and sort + index the result

Inputs:
 None

Outputs:
 None

call bwa mem mapping with single ended reads and sort + index

Inputs:
 None

Outputs:
 None

call bwa mem mapping with paired reads and sort + index the result

Assume -p for bwa if reads2 is None, otherwise specify reads1 and reads2

Inputs:
 None

Outputs:
 None

call bwasw

Inputs:
 None

Outputs:
 None

call bwasw and sort and index the result

Inputs:
 None

Outputs:
 None

call samtools index on a sorted BAM file

Inputs:
 sortedBamFile - full path to sorted bam file

Outputs:
 None

Delete a file without raising an exception

Inputs:
 fileName - full path to file to be removed

Outputs:
 None

Print out the operations and outputs that will be made

Used when the scheduler is in showCommands mode

Inputs:
 None

Outputs:
 None