Test Result : ADAMContextSuite

0 failures (±0) , 2 skipped (±0)
101 tests (±0)
Took 46 sec.

All Tests

Test nameDurationStatus
Can convert from phred0 msPassed
Can convert to phred0 msPassed
Can read a .bed file0.15 secPassed
Can read a .gtf file0.46 secPassed
Can read a .interval_list file0.26 secPassed
Can read a .narrowPeak file0.15 secPassed
Can read a BED 12 file0.17 secPassed
bad glob should fail93 msPassed
can filter a .SAM file based on quality0.21 secPassed
can read a BGZF compressed BCFv2.2 file0 msSkipped
can read a BGZF gzipped .vcf file with .bgz file extension0.18 secPassed
can read a BGZF gzipped .vcf file with .gz file extension0.19 secPassed
can read a SnpEff-annotated .vcf file0.34 secPassed
can read a gzipped .vcf file0.2 secPassed
can read a small .CRAM file0.19 secPassed
can read a small .SAM file0.5 secPassed
can read a small .SAM file with a bad header with lenient validation0.48 secPassed
can read a small .SAM with all attribute tag types0.16 secPassed
can read a small .vcf file0.28 secPassed
can read a small .vcf file with a validation issue0.17 secPassed
can read a vcf file with a projection0.34 secPassed
can read a vcf file with an empty alt0.19 secPassed
can read an uncompressed BCFv2.2 file0 msSkipped
convert program record48 msPassed
ctr is accessible80 msPassed
empty directory should fail67 msPassed
filter on load using the filter2 API1.1 secPassed
import block compressed single fastq0.49 secPassed
import records from interleaved FASTQ: 10.46 secPassed
import records from interleaved FASTQ: 20.44 secPassed
import records from interleaved FASTQ: 30.45 secPassed
import records from interleaved FASTQ: 40.38 secPassed
import records from single ended FASTQ: 10.31 secPassed
import records from single ended FASTQ: 20.33 secPassed
import records from single ended FASTQ: 30.35 secPassed
import records from single ended FASTQ: 40.32 secPassed
load BED features with Bedtools .genome file as sequence dictionary0.25 secPassed
load BED features with Bedtools .genome file as sequence dictionary, no matching features0.2 secPassed
load Bedtools .genome file as sequence dictionary0.17 secPassed
load Bedtools .genome.txt file as sequence dictionary0.16 secPassed
load HTSJDK sequence dictionary91 msPassed
load UCSC Genome Browser chromInfo.txt file as sequence dictionary0.16 secPassed
load alignments from data frame0.63 secPassed
load alignments with metadata from data frame0.7 secPassed
load and save gvcf which contains rows without likelihoods0.32 secPassed
load block compressed interleaved fastq0.81 secPassed
load features from data frame0.69 secPassed
load features with metadata from data frame0.63 secPassed
load fragments from data frame0.91 secPassed
load fragments with metadata from data frame0.85 secPassed
load from an empty directory67 msPassed
load genotypes from data frame with default header lines1 secPassed
load genotypes from data frame with empty header lines1.1 secPassed
load genotypes with metadata from data frame1.1 secPassed
load gvcf which contains a multi-allelic row from a directory0.17 secPassed
load paired fastq0.32 secPassed
load paired fastq as fragments0.43 secPassed
load paired fastq as fragments without cache0.39 secPassed
load paired fastq without cache0.3 secPassed
load parquet with globs0.67 secPassed
load program record from sam file58 msPassed
load query grouped sam as fragments0.28 secPassed
load queryname sorted sam as fragments0.35 secPassed
load reads from data frame0.56 secPassed
load sequences from data frame0.82 secPassed
load slices from data frame1.1 secPassed
load unrecognized file extension as sequence dictionary fails81 msPassed
load variant contexts from data frame with default header lines3.1 secPassed
load variant contexts from data frame with empty header lines3.1 secPassed
load variant contexts with metadata from data frame3 secPassed
load variants from data frame with default header lines0.88 secPassed
load variants from data frame with empty header lines0.84 secPassed
load variants with metadata from data frame0.85 secPassed
load vcf from a directory0.21 secPassed
load vcf with a glob0.39 secPassed
loadAlignments should not fail on single-end and paired-end fastq reads0.49 secPassed
loadBam with a directory0.19 secPassed
loadBam with a glob0.16 secPassed
loadIndexedBam glob should throw exception without an index file74 msPassed
loadIndexedBam should throw exception without an index file82 msPassed
loadIndexedBam should work with indexed file with index naming format <filename>.bai0.16 secPassed
loadIndexedBam with 1 ReferenceRegion0.18 secPassed
loadIndexedBam with multiple ReferenceRegions0.16 secPassed
loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams0.2 secPassed
loadIndexedBam with multiple ReferenceRegions and indexed bams0.18 secPassed
loadIndexedVcf with 1 ReferenceRegion0.2 secPassed
loadIndexedVcf with multiple ReferenceRegions0.17 secPassed
loading a sam file with a bad header and strict stringency should fail85 msPassed
parse annotations for multi-allelic rows0.33 secPassed
read a HLA fasta from GRCh380.62 secPassed
read a fasta file with comments, gaps, and translation stops0.55 secPassed
read a fasta file with long sequences as sequences0.52 secPassed
read a fasta file with long sequences as slices0.71 secPassed
read a fasta file with short sequences as sequences0.44 secPassed
read a fasta file with short sequences as slices0.46 secPassed
read a gzipped fasta file0.83 secPassed
saveAsParquet with file path0.47 secPassed
saveAsParquet with file path, block size, page size0.44 secPassed
saveAsParquet with save args0.46 secPassed
sc.loadParquet should not fail on unmapped reads0.15 secPassed
sc.loadParquet should not load a file without a type specified0.31 secPassed