Class org.broadinstitute.hellbender.utils.codecs.gtf.EnsemblGtfCodecUnitTest

33

tests

0

failures

0

ignored

0.019s

duration

100%

successful

Tests

Test Duration Result
testCanDecode[0](a.tsv, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[10](gencode.v26.annotation.tar.gz, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0.001s passed
testCanDecode[11](gencode.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0.006s passed
testCanDecode[12](gencode.v26.primary_assembly.annotation.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[13](gencode.v26.long_noncoding_RNAs.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0.001s passed
testCanDecode[14](gencode.invalid_short_header.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0s passed
testCanDecode[15](gencode.invalid_malformed_header.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0.001s passed
testCanDecode[16](gencode.invalid_malformed_header_desc.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0.001s passed
testCanDecode[17](gencode.invalid_malformed_header_prov.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0s passed
testCanDecode[18](gencode.invalid_malformed_header_cont.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0.001s passed
testCanDecode[19](gencode.invalid_malformed_header_form.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0s passed
testCanDecode[1](a.table.gz, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[20](gencode.invalid_malformed_header_date.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, true) 0.001s passed
testCanDecode[21](gencode.valid1.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[22](gencode.valid_gencode_file2.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0.001s passed
testCanDecode[23](gencode.and.this.is.a.valid.one.too.table.gtf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[24](Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.44.gtf, /gatkCloneMountPoint/src/test/resources/large/funcotator/ecoli_ds/gencode/ASM584v2/, true) 0.001s passed
testCanDecode[2](a.bed, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[3](a.bcf, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[4](a.hapmap, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[5](a.refseq, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[6](a.beagle, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[7](a.table, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[8](gencode.v26.annotation.gtf.tsv, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testCanDecode[9](gencode.v26.annotation.tgz, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/, false) 0s passed
testDecode[0](/gatkCloneMountPoint/src/test/resources/large/funcotator/ecoli_ds/gencode/ASM584v2/Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.44.gtf, [Chromosome ena gene 190 255 . + . gene_id "b0001"; gene_type "protein_coding"; gene_name "thrL"; gene_source "ena"; Chromosome ena transcript 190 255 . + . gene_id "b0001"; transcript_id "AAC73112"; gene_type "protein_coding"; gene_name "thrL"; transcript_type "protein_coding"; transcript_name "thrL-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena exon 190 255 . + . gene_id "b0001"; transcript_id "AAC73112"; gene_type "protein_coding"; gene_name "thrL"; transcript_type "protein_coding"; transcript_name "thrL-1"; exon_number 1; exon_id "AAC73112-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena CDS 190 252 . + 0 gene_id "b0001"; transcript_id "AAC73112"; gene_type "protein_coding"; gene_name "thrL"; transcript_type "protein_coding"; transcript_name "thrL-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; protein_id "AAC73112"; Chromosome ena start_codon 190 192 . + 0 gene_id "b0001"; transcript_id "AAC73112"; gene_type "protein_coding"; gene_name "thrL"; transcript_type "protein_coding"; transcript_name "thrL-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; Chromosome ena stop_codon 253 255 . + 0 gene_id "b0001"; transcript_id "AAC73112"; gene_type "protein_coding"; gene_name "thrL"; transcript_type "protein_coding"; transcript_name "thrL-1"; exon_number 1; gene_source "ena"; transcript_source "ena";, Chromosome ena gene 337 2799 . + . gene_id "b0002"; gene_type "protein_coding"; gene_name "thrA"; gene_source "ena"; Chromosome ena transcript 337 2799 . + . gene_id "b0002"; transcript_id "AAC73113"; gene_type "protein_coding"; gene_name "thrA"; transcript_type "protein_coding"; transcript_name "thrA-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena exon 337 2799 . + . gene_id "b0002"; transcript_id "AAC73113"; gene_type "protein_coding"; gene_name "thrA"; transcript_type "protein_coding"; transcript_name "thrA-1"; exon_number 1; exon_id "AAC73113-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena CDS 337 2796 . + 0 gene_id "b0002"; transcript_id "AAC73113"; gene_type "protein_coding"; gene_name "thrA"; transcript_type "protein_coding"; transcript_name "thrA-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; protein_id "AAC73113"; Chromosome ena start_codon 337 339 . + 0 gene_id "b0002"; transcript_id "AAC73113"; gene_type "protein_coding"; gene_name "thrA"; transcript_type "protein_coding"; transcript_name "thrA-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; Chromosome ena stop_codon 2797 2799 . + 0 gene_id "b0002"; transcript_id "AAC73113"; gene_type "protein_coding"; gene_name "thrA"; transcript_type "protein_coding"; transcript_name "thrA-1"; exon_number 1; gene_source "ena"; transcript_source "ena";, Chromosome ena gene 2801 3733 . + . gene_id "b0003"; gene_type "protein_coding"; gene_name "thrB"; gene_source "ena"; Chromosome ena transcript 2801 3733 . + . gene_id "b0003"; transcript_id "AAC73114"; gene_type "protein_coding"; gene_name "thrB"; transcript_type "protein_coding"; transcript_name "thrB-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena exon 2801 3733 . + . gene_id "b0003"; transcript_id "AAC73114"; gene_type "protein_coding"; gene_name "thrB"; transcript_type "protein_coding"; transcript_name "thrB-1"; exon_number 1; exon_id "AAC73114-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena CDS 2801 3730 . + 0 gene_id "b0003"; transcript_id "AAC73114"; gene_type "protein_coding"; gene_name "thrB"; transcript_type "protein_coding"; transcript_name "thrB-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; protein_id "AAC73114"; Chromosome ena start_codon 2801 2803 . + 0 gene_id "b0003"; transcript_id "AAC73114"; gene_type "protein_coding"; gene_name "thrB"; transcript_type "protein_coding"; transcript_name "thrB-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; Chromosome ena stop_codon 3731 3733 . + 0 gene_id "b0003"; transcript_id "AAC73114"; gene_type "protein_coding"; gene_name "thrB"; transcript_type "protein_coding"; transcript_name "thrB-1"; exon_number 1; gene_source "ena"; transcript_source "ena";, Chromosome ena gene 3734 5020 . + . gene_id "b0004"; gene_type "protein_coding"; gene_name "thrC"; gene_source "ena"; Chromosome ena transcript 3734 5020 . + . gene_id "b0004"; transcript_id "AAC73115"; gene_type "protein_coding"; gene_name "thrC"; transcript_type "protein_coding"; transcript_name "thrC-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena exon 3734 5020 . + . gene_id "b0004"; transcript_id "AAC73115"; gene_type "protein_coding"; gene_name "thrC"; transcript_type "protein_coding"; transcript_name "thrC-1"; exon_number 1; exon_id "AAC73115-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena CDS 3734 5017 . + 0 gene_id "b0004"; transcript_id "AAC73115"; gene_type "protein_coding"; gene_name "thrC"; transcript_type "protein_coding"; transcript_name "thrC-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; protein_id "AAC73115"; Chromosome ena start_codon 3734 3736 . + 0 gene_id "b0004"; transcript_id "AAC73115"; gene_type "protein_coding"; gene_name "thrC"; transcript_type "protein_coding"; transcript_name "thrC-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; Chromosome ena stop_codon 5018 5020 . + 0 gene_id "b0004"; transcript_id "AAC73115"; gene_type "protein_coding"; gene_name "thrC"; transcript_type "protein_coding"; transcript_name "thrC-1"; exon_number 1; gene_source "ena"; transcript_source "ena";, Chromosome ena gene 5234 5530 . + . gene_id "b0005"; gene_type "protein_coding"; gene_name "yaaX"; gene_source "ena"; Chromosome ena transcript 5234 5530 . + . gene_id "b0005"; transcript_id "AAC73116"; gene_type "protein_coding"; gene_name "yaaX"; transcript_type "protein_coding"; transcript_name "yaaX-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena exon 5234 5530 . + . gene_id "b0005"; transcript_id "AAC73116"; gene_type "protein_coding"; gene_name "yaaX"; transcript_type "protein_coding"; transcript_name "yaaX-1"; exon_number 1; exon_id "AAC73116-1"; gene_source "ena"; transcript_source "ena"; Chromosome ena CDS 5234 5527 . + 0 gene_id "b0005"; transcript_id "AAC73116"; gene_type "protein_coding"; gene_name "yaaX"; transcript_type "protein_coding"; transcript_name "yaaX-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; protein_id "AAC73116"; Chromosome ena start_codon 5234 5236 . + 0 gene_id "b0005"; transcript_id "AAC73116"; gene_type "protein_coding"; gene_name "yaaX"; transcript_type "protein_coding"; transcript_name "yaaX-1"; exon_number 1; gene_source "ena"; transcript_source "ena"; Chromosome ena stop_codon 5528 5530 . + 0 gene_id "b0005"; transcript_id "AAC73116"; gene_type "protein_coding"; gene_name "yaaX"; transcript_type "protein_coding"; transcript_name "yaaX-1"; exon_number 1; gene_source "ena"; transcript_source "ena";], ASM584v2) 0.005s passed
testValidateHeader[0]([], true) 0s passed
testValidateHeader[1]([, , , , ], false) 0s passed
testValidateHeader[2]([#!genome-build ASM584v2, #!genome-version ASM584v2, #!genome-date 2014-08, #!genome-build-accession GCA_000005845.2, #!genebuild-last-updated 2014-08], true) 0s passed
testValidateHeader[3]([##genome-build ASM584v2, ##genome-version ASM584v2, ##genome-date 2014-08, ##genome-build-accession GCA_000005845.2, ##genebuild-last-updated 2014-08], true) 0s passed
testValidateHeader[4]([##genome-build ASM584v2, ##genome-version ASM584v2, #!genome-date 2014-08, ##genome-build-accession GCA_000005845.2, #!genebuild-last-updated 2014-08], true) 0s passed
testValidateHeader[5]([##genome-build ASM584v2, ##genome-version ASM584v2, genome-date 2014-08, ##genome-build-accession GCA_000005845.2, ##genebuild-last-updated 2014-08], false) 0s passed
testValidateHeader[6]([##genome-build ASM584v2, #!genome-version ASM584v2, genome-date 2014-08, ##genome-build-accession GCA_000005845.2, #!genebuild-last-updated 2014-08], false) 0s passed

Standard error

21:27:06.624 WARN  AbstractGtfCodec - Caught IOException on file: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/gencode.gtf - returning can decode as failure.
21:27:06.628 WARN  AbstractGtfCodec - Caught IOException on file: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/gencode.gtf - returning can decode as failure.
21:27:06.628 WARN  AbstractGtfCodec - Caught IOException on file: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/gencode.v26.primary_assembly.annotation.gtf - returning can decode as failure.
21:27:06.628 WARN  AbstractGtfCodec - Caught IOException on file: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/gencode.v26.primary_assembly.annotation.gtf - returning can decode as failure.
21:27:06.628 WARN  AbstractGtfCodec - Caught IOException on file: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/gencode.v26.long_noncoding_RNAs.gtf - returning can decode as failure.
21:27:06.628 WARN  AbstractGtfCodec - Caught IOException on file: /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/gtf/gencode.v26.long_noncoding_RNAs.gtf - returning can decode as failure.