def _get_hetcallers(items): out = set([]) for d in items: hetcaller = dd.get_hetcaller(d) if hetcaller: out = out.union(set(hetcaller)) return sorted(list(out))
def _ready_for_het_analysis(items): """Check if a sample has input information for heterogeneity analysis. We currently require a tumor/normal sample containing both CNV and variant calls. """ paired = vcfutils.get_paired_bams([dd.get_align_bam(d) for d in items], items) has_het = any(dd.get_hetcaller(d) for d in items) if has_het and paired: return _get_variants(paired.tumor_data) and _get_calls(paired.tumor_data, cnv_only=True)
def _ready_for_het_analysis(items): """Check if a sample has input information for heterogeneity analysis. We currently require a tumor/normal sample containing both CNV and variant calls. """ paired = vcfutils.get_paired_bams([dd.get_align_bam(d) for d in items], items) has_het = any(dd.get_hetcaller(d) for d in items) if has_het and paired: return get_variants(paired.tumor_data) and _get_calls( paired.tumor_data, cnv_only=True)