public void Merge_same_histology_site()
{
var chrom = new Chromosome("chrW", "W", 1);
var item1 = new CosmicCnvItem(1, chrom, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>()
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>()
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
var item2 = new CosmicCnvItem(1, chrom, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>()
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>()
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 2);
item1.Merge(item2);
Assert.Equal(2, item1.CancerTypeCount);
Assert.Equal(2, item1.TissueTypeCount);
}
public void Merge_throws_exception_if_cnvs_differ()
{
var chrom = new Chromosome("chrW", "W", 1);
var item1 = new CosmicCnvItem(1, chrom, 100, 1000, VariantType.copy_number_loss, 0,
new Dictionary <string, int>()
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>()
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
var item2 = new CosmicCnvItem(1, chrom, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>()
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>()
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
Assert.Throws <InvalidDataException>(() => item1.Merge(item2));
}
public void Merge_check_adjust_counts()
{
var chrom = new Chromosome("chrW", "W", 1);
var item1 = new CosmicCnvItem(1, chrom, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>()
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>()
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
var item2 = new CosmicCnvItem(1, chrom, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>()
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>()
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 2);
item1.Merge(item2);
Assert.Equal("\"id\":1,\"variantType\":\"copy_number_gain\",\"copyNumber\":3,\"cancerTypes\":[{\"histology1\":2},{\"histology2\":4}],\"tissueTypes\":[{\"tissue1\":4},{\"tissue2\":2}]", item1.GetJsonString());
}
public void Merge_add_new_items()
{
var item1 = new CosmicCnvItem(1, ChromosomeUtilities.Chr1, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
var item2 = new CosmicCnvItem(1, ChromosomeUtilities.Chr1, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>
{
{ "histology3", 1 },
{ "histology4", 2 }
}, new Dictionary <string, int>
{
{ "tissue3", 2 },
{ "tissue4", 1 }
}, 2);
item1.Merge(item2);
Assert.Equal(4, item1.CancerTypeCount);
Assert.Equal(4, item1.TissueTypeCount);
}
public void Merge_avoid_double_counting()
{
var item1 = new CosmicCnvItem(1, ChromosomeUtilities.Chr1, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
var item2 = new CosmicCnvItem(1, ChromosomeUtilities.Chr1, 100, 1000, VariantType.copy_number_gain, 3,
new Dictionary <string, int>
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 1);
item1.Merge(item2);
Assert.Equal("\"id\":1,\"variantType\":\"copy_number_gain\",\"copyNumber\":3,\"cancerTypes\":[{\"histology1\":1},{\"histology2\":2}],\"tissueTypes\":[{\"tissue1\":2},{\"tissue2\":1}]", item1.GetJsonString());
}
public void GetJsonString_unspecified_copy_number()
{
var item1 = new CosmicCnvItem(1, ChromosomeUtilities.Chr1, 100, 1000, VariantType.copy_number_gain, -1,
new Dictionary <string, int>
{
{ "histology1", 1 },
{ "histology2", 2 }
}, new Dictionary <string, int>
{
{ "tissue1", 2 },
{ "tissue2", 1 }
}, 2);
Assert.Equal("\"id\":1,\"variantType\":\"copy_number_gain\",\"cancerTypes\":[{\"histology1\":1},{\"histology2\":2}],\"tissueTypes\":[{\"tissue1\":2},{\"tissue2\":1}]", item1.GetJsonString());
}
