def __init__(self,
pool,
sample,
fileName=None,
sam=False,
sortedBam=False,
headerLine=False,
duplicates=True,
mdTag=False,
index=False):
"""The constructor of the bam file sets all default vaules of the instance variables
:param sam: boolean whether this file is a sam or bam file
:param sortedBam: boolean whether this file is sorted or not
:param headerLine: boolean whether this file contains an @rg tag
:param duplicates: boolean whether the possible pcr duplicates are already removed
:param mdTag: boolean whether the md tag is already added to this file
:param index: whether there is already created an index of this bam file
"""
self.sam = sam
self.sorted = sortedBam
self.headerLine = headerLine
self.duplicates = duplicates
self.mdTag = mdTag
self.index = index
self.gridJob = ClusterJob.getClusterJob(pool, sample)
super(BamFile, self).__init__(pool, sample, fileName)
def __init__(self, pool, sample, fileName=None, forward=True, hq=False):
"""The constructor of the fastq file sets the variable whether the quality control is done.
:param hq: Whether the quality control is already done on this file, so the reads all have a High Quality
:param forward: Whether this fastq file are the forward reads or the reversed reads
"""
super(FastqFile, self).__init__(pool, sample=sample, fileName=fileName)
self.hq = hq
self.forward = forward
self.gridJob = ClusterJob.getClusterJob(pool, sample)
def __init__(self, pool, sample, fileName=None, forward=True, hq=False):
"""The constructor of the fastq file sets the variable whether the quality control is done.
:param hq: Whether the quality control is already done on this file, so the reads all have a High Quality
:param forward: Whether this fastq file are the forward reads or the reversed reads
"""
super(FastqFile,self).__init__(pool, sample=sample, fileName=fileName)
self.hq = hq
self.forward = forward
self.gridJob = ClusterJob.getClusterJob(pool, sample)
def __init__(self, pool, fileName=None, bcf = False, filtered = False, phased=False, chrom=None):
"""The constructor of the vcf file sets the given variables as instance variables.
:param bcf: boolean whether the file is bcf or vcf, default: True
:param filtered: boolean whether the file is already filtered or not, default: True
"""
self.bcf = bcf
self.chrom = chrom
self.filtered = filtered
self.phased = phased
super(VcfFile,self).__init__(pool, fileName=fileName)
self.gridJob = ClusterJob.getClusterJob(pool, chrom=chrom)
def __init__(self,pool, sample, fileName=None, sam=False, sortedBam = False, headerLine = False, duplicates = True, mdTag = False, index = False):
"""The constructor of the bam file sets all default vaules of the instance variables
:param sam: boolean whether this file is a sam or bam file
:param sortedBam: boolean whether this file is sorted or not
:param headerLine: boolean whether this file contains an @rg tag
:param duplicates: boolean whether the possible pcr duplicates are already removed
:param mdTag: boolean whether the md tag is already added to this file
:param index: whether there is already created an index of this bam file
"""
self.sam = sam
self.sorted = sortedBam
self.headerLine = headerLine
self.duplicates = duplicates
self.mdTag = mdTag
self.index = index
self.gridJob = ClusterJob.getClusterJob(pool, sample)
super(BamFile,self).__init__(pool, sample,fileName)
def __init__(self, pool, chrom, fileName = None, beageleInput=True):
"""The constructor of the BeagleFile sets the instance variables.
:param chrom: The name of the chromosome
:type chrom: str
"""
self.chrom = chrom
self.beageleInput = beageleInput
super(BeagleFile,self).__init__(pool, fileName=fileName)
self.gridJob = ClusterJob.getClusterJob(pool, chrom=chrom)
if beageleInput == False:
self.setFile(fileName)
else:
self.doseFile = None
self.gprobsFile = None
self.phasedFile = None
self.rTwoFile = None
def __init__(self, pool, chrom, fileName=None, beageleInput=True):
"""The constructor of the BeagleFile sets the instance variables.
:param chrom: The name of the chromosome
:type chrom: str
"""
self.chrom = chrom
self.beageleInput = beageleInput
super(BeagleFile, self).__init__(pool, fileName=fileName)
self.gridJob = ClusterJob.getClusterJob(pool, chrom=chrom)
if beageleInput == False:
self.setFile(fileName)
else:
self.doseFile = None
self.gprobsFile = None
self.phasedFile = None
self.rTwoFile = None
