def _from_java(cls, jrep):
gr = GenomeReference.__new__(cls)
gr._init_from_java(jrep)
gr._name = jrep.name()
gr._contigs = [str(x) for x in jrep.contigs()]
gr._lengths = {str(x._1()): int(x._2()) for x in jiterable_to_list(jrep.lengths())}
gr._x_contigs = [str(x) for x in jiterable_to_list(jrep.xContigs())]
gr._y_contigs = [str(x) for x in jiterable_to_list(jrep.yContigs())]
gr._mt_contigs = [str(x) for x in jiterable_to_list(jrep.mtContigs())]
gr._par = [Interval._from_java(x) for x in jrep.par()]
return gr
def _from_java(cls, jrep):
gr = GenomeReference.__new__(cls)
gr._init_from_java(jrep)
gr._name = jrep.name()
gr._contigs = [str(x) for x in jrep.contigs()]
gr._lengths = {
str(x._1()): int(x._2())
for x in jiterable_to_list(jrep.lengths())
}
gr._x_contigs = [str(x) for x in jiterable_to_list(jrep.xContigs())]
gr._y_contigs = [str(x) for x in jiterable_to_list(jrep.yContigs())]
gr._mt_contigs = [str(x) for x in jiterable_to_list(jrep.mtContigs())]
gr._par = [Interval._from_java(x) for x in jrep.par()]
return gr
def _from_java(cls, jrep):
summary = Summary.__new__(cls)
summary.samples = jrep.samples()
summary.variants = jrep.variants()
summary.call_rate = jrep.callRate().getOrElse(None)
summary.contigs = [str(x) for x in jiterable_to_list(jrep.contigs())]
summary.multiallelics = jrep.multiallelics()
summary.snps = jrep.snps()
summary.mnps = jrep.mnps()
summary.insertions = jrep.insertions()
summary.deletions = jrep.deletions()
summary.complex = jrep.complex()
summary.star = jrep.star()
summary.max_alleles = jrep.maxAlleles()
return summary
def _from_java(cls, jrep):
summary = Summary.__new__(cls)
summary.samples = jrep.samples()
summary.variants = jrep.variants()
summary.call_rate = jrep.callRate().get() if jrep.callRate().isDefined() else float('nan')
summary.contigs = [str(x) for x in jiterable_to_list(jrep.contigs())]
summary.multiallelics = jrep.multiallelics()
summary.snps = jrep.snps()
summary.mnps = jrep.mnps()
summary.insertions = jrep.insertions()
summary.deletions = jrep.deletions()
summary.complex = jrep.complex()
summary.star = jrep.star()
summary.max_alleles = jrep.maxAlleles()
return summary