module
biopipen.utils.vcf
Classes
HeaderItem— The base class of header items</>HeaderInfo— The INFO items in the header</>HeaderFormat— The FORMAT items in the header</>HeaderFilter— The FILTER items in the header</>HeaderContig— The contig items in the header</>HeaderGeneral— The general items in the header</>Fields— The fields/column names</>Info— The INFO of the variant</>Format— The FORMAT of the variant</>Alt— The ALT of the variant</>Filter— The FILTER of the variant</>Sample— One sample of the variant</>Samples— The samples of the variant</>
class
biopipen.utils.vcf.HeaderItem(*args, **kwargs)
Bases
dict
The base class of header items
class
biopipen.utils.vcf.HeaderInfo(*args, **kwargs)
Bases
The INFO items in the header
class
biopipen.utils.vcf.HeaderFormat(*args, **kwargs)
Bases
The FORMAT items in the header
class
biopipen.utils.vcf.HeaderFilter(*args, **kwargs)
Bases
The FILTER items in the header
class
biopipen.utils.vcf.HeaderContig(*args, **kwargs)
Bases
The contig items in the header
class
biopipen.utils.vcf.HeaderGeneral(*args, **kwargs)
Bases
The general items in the header
class
biopipen.utils.vcf.Fields(*args, **kwargs)
Bases
list
The fields/column names
class
biopipen.utils.vcf.Info()
Bases
dict
The INFO of the variant
class
biopipen.utils.vcf.Format(iterable=())
Bases
list
The FORMAT of the variant
class
biopipen.utils.vcf.Alt(iterable=())
Bases
list
The ALT of the variant
class
biopipen.utils.vcf.Filter(iterable=())
Bases
list
The FILTER of the variant
class
biopipen.utils.vcf.Sample(values, format)
Bases
dict
One sample of the variant
class
biopipen.utils.vcf.Samples(samples, format)
Bases
list
The samples of the variant