gosling.BamData

class gosling.BamData(indexUrl=Undefined, type=Undefined, url=Undefined, extractJunction=Undefined, junctionMinCoverage=Undefined, loadMates=Undefined, maxInsertSize=Undefined, **kwds)

BamData schema wrapper

Mapping(required=[type, url, indexUrl]) Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files.

Attributes:

indexUrlstring

URL link to the index file of the BAM file

typestring

urlstring

URL link to the BAM data file

extractJunctionboolean

Determine whether to extract exon-to-exon junctions. __Default__: false

junctionMinCoveragefloat

Determine the threshold of coverage when extracting exon-to-exon junctions. __Default__: 1

loadMatesboolean

Load mates that are located in the same chromosome. __Default__: false

maxInsertSizefloat

Determines the threshold of insert sizes for determining the structural variants. __Default__: 5000

__init__(indexUrl=Undefined, type=Undefined, url=Undefined, extractJunction=Undefined, junctionMinCoverage=Undefined, loadMates=Undefined, maxInsertSize=Undefined, **kwds)

Methods

__init__([indexUrl, type, url, ...])
copy([deep, ignore])	Return a copy of the object
from_dict(dct[, validate, _wrapper_classes])	Construct class from a dictionary representation
from_json(json_string[, validate])	Instantiate the object from a valid JSON string
resolve_references([schema])	Resolve references in the context of this object's schema or root schema.
to_dict([validate, ignore, context])	Return a dictionary representation of the object
to_json([validate, ignore, context, indent, ...])	Emit the JSON representation for this object as a string.
validate(instance[, schema])	Validate the instance against the class schema in the context of the rootschema.
validate_property(name, value[, schema])	Validate a property against property schema in the context of the rootschema