| Test |
Duration |
Result |
| testAliasingErrors[0]({}, {}, [], false, {}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={ATTR1=VAL_ATTR1} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3) |
0s |
passed |
| testAliasingErrors[1]({}, {}, [CONTIG, START, foo], false, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3) |
0s |
passed |
| testAliasingErrors[2]({}, {}, [], false, {}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3) |
0s |
passed |
| testAliasing[0]({}, {}, [], true, {}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [CONTIG, END, START, TO_BE_ALIASED1], [CONTIG, END, START, TO_BE_ALIASED1], [3, 3200000, 2100000, value1]) |
0.001s |
passed |
| testAliasing[10]({}, {}, [CONTIG, START], false, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo], [TO_BE_ALIASED1], [value1]) |
0.001s |
passed |
| testAliasing[11]({foo=BAD_DEFAULT, foo2=val2, foo3=val3}, {}, [], false, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, foo2, foo3], [TO_BE_ALIASED1, foo2, foo3], [value1, val2, val3]) |
0.001s |
passed |
| testAliasing[12]({}, {foo=OVERRIDE, foo2=val2, foo3=val3}, [], false, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, foo2, foo3], [TO_BE_ALIASED1, foo2, foo3], [OVERRIDE, val2, val3]) |
0.001s |
passed |
| testAliasing[13]({}, {foo=OVERRIDE, foo2=val2, foo3=val3}, [foo2, foo3], false, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo], [TO_BE_ALIASED1], [OVERRIDE]) |
0s |
passed |
| testAliasing[14]({}, {}, [CONTIG, START], true, {foo=[DUMMY1, DUMMY2, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, END, TO_BE_ALIASED1], [, END, TO_BE_ALIASED1], [__UNKNOWN__, 3200000, value1]) |
0s |
passed |
| testAliasing[15]({}, {}, [CONTIG, START], false, {foo=[DUMMY1, DUMMY2, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo], [], [__UNKNOWN__]) |
0.001s |
passed |
| testAliasing[16]({}, {}, [CONTIG, START, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar, END, TO_BE_ALIASED1], [, END, TO_BE_ALIASED1], [__UNKNOWN__, 3200000, value1]) |
0.001s |
passed |
| testAliasing[17]({}, {}, [CONTIG, START, foo], false, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar], [], [__UNKNOWN__]) |
0.001s |
passed |
| testAliasing[18]({}, {}, [CONTIG, START, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[TO_BE_ALIASED1, DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar, END], [TO_BE_ALIASED1, END], [value1, 3200000]) |
0.001s |
passed |
| testAliasing[19]({}, {}, [CONTIG, START, foo], false, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[TO_BE_ALIASED1, DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar], [TO_BE_ALIASED1], [value1]) |
0s |
passed |
| testAliasing[1]({}, {}, [], true, {foo=[TO_BE_ALIASED1]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, CONTIG, END, START], [TO_BE_ALIASED1, CONTIG, END, START], [value1, 3, 3200000, 2100000]) |
0.001s |
passed |
| testAliasing[20]({}, {}, [CONTIG, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[TO_BE_ALIASED1, DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar, END, START], [TO_BE_ALIASED1, END, START], [value1, 3200000, 2100000]) |
0.001s |
passed |
| testAliasing[21]({foo=DEFAULT, bar=val2, foo3=val3}, {}, [CONTIG, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[TO_BE_ALIASED1, DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar, END, START, foo3], [TO_BE_ALIASED1, END, START, foo3], [value1, 3200000, 2100000, val3]) |
0.001s |
passed |
| testAliasing[22]({foo=DEFAULT, bar=val2, foo3=val3, foo1=val1, foo10=val10}, {}, [CONTIG, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[TO_BE_ALIASED1, DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar, END, START, foo1, foo3, foo10], [TO_BE_ALIASED1, END, START, foo1, foo3, foo10], [value1, 3200000, 2100000, val1, val3, val10]) |
0.001s |
passed |
| testAliasing[23]({foo=DEFAULT, bar=val2, foo1=val1, foo10=val10}, {foo3=val3}, [CONTIG, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], bar=[TO_BE_ALIASED1, DUMMY3, DUMMY4, DUMMY5]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [bar, END, START, foo1, foo3, foo10], [TO_BE_ALIASED1, END, START, foo1, foo3, foo10], [value1, 3200000, 2100000, val1, val3, val10]) |
0s |
passed |
| testAliasing[24]({foo=DEFAULT, bar=val2, foo3=val3, foo1=val1, foo10=val10}, {}, [CONTIG, foo], true, {foo=[DUMMY1, DUMMY2, DUMMY3], foo3=[DUMMY03, DUMMY04, DUMMY05], foo1=[DUMMY13, DUMMY14, DUMMY15], foo10=[DUMMY23, DUMMY24, DUMMY25], bar=[TO_BE_ALIASED1, DUMMY33, DUMMY34, DUMMY35]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo3, foo1, foo10, bar, END, START], [, , , TO_BE_ALIASED1, END, START], [val3, val1, val10, value1, 3200000, 2100000]) |
0s |
passed |
| testAliasing[2]({}, {}, [], true, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, CONTIG, END, START], [TO_BE_ALIASED1, CONTIG, END, START], [value1, 3, 3200000, 2100000]) |
0.001s |
passed |
| testAliasing[3]({}, {}, [CONTIG, START], true, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, END], [TO_BE_ALIASED1, END], [value1, 3200000]) |
0s |
passed |
| testAliasing[4]({}, {}, [CONTIG, START, foo], true, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [END], [END], [3200000]) |
0.001s |
passed |
| testAliasing[5]({foo=BAD_DEFAULT, foo2=val2, foo3=val3}, {}, [], true, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, CONTIG, END, START, foo2, foo3], [TO_BE_ALIASED1, CONTIG, END, START, foo2, foo3], [value1, 3, 3200000, 2100000, val2, val3]) |
0.001s |
passed |
| testAliasing[6]({}, {foo=OVERRIDE, foo2=val2, foo3=val3}, [], true, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, CONTIG, END, START, foo2, foo3], [TO_BE_ALIASED1, CONTIG, END, START, foo2, foo3], [OVERRIDE, 3, 3200000, 2100000, val2, val3]) |
0s |
passed |
| testAliasing[7]({}, {foo=OVERRIDE, foo2=val2, foo3=val3}, [foo2, foo3], true, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo, CONTIG, END, START], [TO_BE_ALIASED1, CONTIG, END, START], [OVERRIDE, 3, 3200000, 2100000]) |
0.001s |
passed |
| testAliasing[8]({}, {}, [], false, {foo=[TO_BE_ALIASED1]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo], [TO_BE_ALIASED1], [value1]) |
0.001s |
passed |
| testAliasing[9]({}, {}, [], false, {foo=[DUMMY1, DUMMY2, TO_BE_ALIASED1, DUMMY3]}, [VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=, org.broadinstitute.hellbender.tools.funcotator.FuncotationMap@58fbe1b3, [foo], [TO_BE_ALIASED1], [value1]) |
0s |
passed |
| testLoadingConfigFile[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/test_tsv_output.config, {genes=[Gencode_19_genes], foo1=[], foo2=[TEST2, foobar2], foo3=[TEST3, foobar2], foo3!!=[]}) |
0.001s |
passed |
| testLoadingConfigFile[1](/tmp/tmp_read_resource_5530721118948760536.config, {alt_allele=[Gencode_19_alt_allele, Gencode_27_alt_allele, Gencode_28_alt_allele], end_gene=[Gencode_19_end_gene, Gencode_27_end_gene, Gencode_28_end_gene], end=[END, End, End_Position, end_position, chromEnd, segment_end, End_position, target_end, stop, Stop, Position, position, pos, POS, segment_end], start_gene=[Gencode_19_start_gene, Gencode_27_start_gene, Gencode_28_start_gene], Segment_Mean=[MEAN_LOG2_COPY_RATIO], genes=[Gencode_19_genes, Gencode_27_genes, Gencode_28_genes], Sample=[sample, sample_id], start=[START, Start, Start_Position, start_position, chromStart, segment_start, Start_position, target_start, Position, position, pos, POS, segment_start], chr=[CONTIG, contig, Chromosome, chrom, chromosome, Chrom, seqname, seqnames, CHROM, target_contig, segment_contig], build=[], Num_Probes=[NUM_POINTS_COPY_RATIO], start_exon=[Gencode_19_start_exon, Gencode_27_start_exon, Gencode_28_start_exon], end_exon=[Gencode_19_end_exon, Gencode_27_end_exon, Gencode_28_end_exon], ref_allele=[Gencode_19_ref_allele, Gencode_27_ref_allele, Gencode_28_ref_allele], Segment_Call=[]}) |
0.001s |
passed |
| testSimpleSegFileWriting[0]([VC /tmp/funcotatorTmpFolder13669890650518203127/GRCh37.p13.chr3.fasta @ 3:2100000-3200000 Q. of type=SYMBOLIC alleles=[T*, <COPY_NEUTRAL>] attr={} GT=[] filters=) |
0.001s |
passed |