| Can convert from phred | 1 ms | Passed |
| Can convert to phred | 0 ms | Passed |
| Can read a .bed file | 0.22 sec | Passed |
| Can read a .gtf file | 0.49 sec | Passed |
| Can read a .interval_list file | 0.28 sec | Passed |
| Can read a .narrowPeak file | 0.18 sec | Passed |
| Can read a BED 12 file | 0.17 sec | Passed |
| bad glob should fail | 67 ms | Passed |
| can filter a .SAM file based on quality | 0.25 sec | Passed |
| can read a BGZF compressed BCFv2.2 file | 0 ms | Skipped |
| can read a BGZF gzipped .vcf file with .bgz file extension | 0.19 sec | Passed |
| can read a BGZF gzipped .vcf file with .gz file extension | 0.18 sec | Passed |
| can read a SnpEff-annotated .vcf file | 0.29 sec | Passed |
| can read a gzipped .vcf file | 0.19 sec | Passed |
| can read a small .CRAM file | 0.34 sec | Passed |
| can read a small .SAM file | 0.45 sec | Passed |
| can read a small .SAM file with a bad header with lenient validation | 0.68 sec | Passed |
| can read a small .SAM with all attribute tag types | 0.42 sec | Passed |
| can read a small .vcf file | 0.29 sec | Passed |
| can read a small .vcf file with a validation issue | 0.18 sec | Passed |
| can read a vcf file with a projection | 0.26 sec | Passed |
| can read a vcf file with an empty alt | 0.23 sec | Passed |
| can read an uncompressed BCFv2.2 file | 0 ms | Skipped |
| convert program record | 53 ms | Passed |
| ctr is accessible | 95 ms | Passed |
| empty directory should fail | 68 ms | Passed |
| filter on load using the filter2 API | 1.2 sec | Passed |
| import block compressed single fastq | 0.39 sec | Passed |
| import records from interleaved FASTQ: 1 | 0.53 sec | Passed |
| import records from interleaved FASTQ: 2 | 0.41 sec | Passed |
| import records from interleaved FASTQ: 3 | 0.39 sec | Passed |
| import records from interleaved FASTQ: 4 | 0.38 sec | Passed |
| import records from single ended FASTQ: 1 | 0.25 sec | Passed |
| import records from single ended FASTQ: 2 | 0.27 sec | Passed |
| import records from single ended FASTQ: 3 | 0.27 sec | Passed |
| import records from single ended FASTQ: 4 | 0.26 sec | Passed |
| load BED features with Bedtools .genome file as sequence dictionary | 0.19 sec | Passed |
| load BED features with Bedtools .genome file as sequence dictionary, no matching features | 0.23 sec | Passed |
| load Bedtools .genome file as sequence dictionary | 0.16 sec | Passed |
| load Bedtools .genome.txt file as sequence dictionary | 0.19 sec | Passed |
| load HTSJDK sequence dictionary | 72 ms | Passed |
| load UCSC Genome Browser chromInfo.txt file as sequence dictionary | 0.13 sec | Passed |
| load alignments from data frame | 0.8 sec | Passed |
| load alignments with metadata from data frame | 0.66 sec | Passed |
| load and save gvcf which contains rows without likelihoods | 0.26 sec | Passed |
| load block compressed interleaved fastq | 0.6 sec | Passed |
| load features from data frame | 0.68 sec | Passed |
| load features with metadata from data frame | 0.66 sec | Passed |
| load fragments from data frame | 0.85 sec | Passed |
| load fragments with metadata from data frame | 0.86 sec | Passed |
| load from an empty directory | 0.1 sec | Passed |
| load genotypes from data frame with default header lines | 1 sec | Passed |
| load genotypes from data frame with empty header lines | 1 sec | Passed |
| load genotypes with metadata from data frame | 1.2 sec | Passed |
| load gvcf which contains a multi-allelic row from a directory | 0.18 sec | Passed |
| load paired fastq | 0.29 sec | Passed |
| load paired fastq as fragments | 0.33 sec | Passed |
| load paired fastq as fragments without cache | 0.35 sec | Passed |
| load paired fastq without cache | 0.36 sec | Passed |
| load parquet with globs | 0.53 sec | Passed |
| load program record from sam file | 63 ms | Passed |
| load query grouped sam as fragments | 0.21 sec | Passed |
| load queryname sorted sam as fragments | 0.26 sec | Passed |
| load reads from data frame | 0.63 sec | Passed |
| load sequences from data frame | 0.88 sec | Passed |
| load slices from data frame | 1.1 sec | Passed |
| load unrecognized file extension as sequence dictionary fails | 74 ms | Passed |
| load variant contexts from data frame with default header lines | 3.2 sec | Passed |
| load variant contexts from data frame with empty header lines | 3.4 sec | Passed |
| load variant contexts with metadata from data frame | 3.5 sec | Passed |
| load variants from data frame with default header lines | 0.85 sec | Passed |
| load variants from data frame with empty header lines | 0.83 sec | Passed |
| load variants with metadata from data frame | 0.91 sec | Passed |
| load vcf from a directory | 0.2 sec | Passed |
| load vcf with a glob | 0.39 sec | Passed |
| loadAlignments should not fail on single-end and paired-end fastq reads | 0.41 sec | Passed |
| loadBam with a directory | 0.16 sec | Passed |
| loadBam with a glob | 0.15 sec | Passed |
| loadIndexedBam glob should throw exception without an index file | 68 ms | Passed |
| loadIndexedBam should throw exception without an index file | 64 ms | Passed |
| loadIndexedBam should work with indexed file with index naming format <filename>.bai | 0.13 sec | Passed |
| loadIndexedBam with 1 ReferenceRegion | 0.16 sec | Passed |
| loadIndexedBam with multiple ReferenceRegions | 0.13 sec | Passed |
| loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams | 0.14 sec | Passed |
| loadIndexedBam with multiple ReferenceRegions and indexed bams | 0.12 sec | Passed |
| loadIndexedVcf with 1 ReferenceRegion | 0.47 sec | Passed |
| loadIndexedVcf with multiple ReferenceRegions | 0.16 sec | Passed |
| loading a sam file with a bad header and strict stringency should fail | 0.1 sec | Passed |
| parse annotations for multi-allelic rows | 0.28 sec | Passed |
| read a HLA fasta from GRCh38 | 0.63 sec | Passed |
| read a fasta file with comments, gaps, and translation stops | 0.62 sec | Passed |
| read a fasta file with long sequences as sequences | 0.52 sec | Passed |
| read a fasta file with long sequences as slices | 0.68 sec | Passed |
| read a fasta file with short sequences as sequences | 0.37 sec | Passed |
| read a fasta file with short sequences as slices | 0.45 sec | Passed |
| read a gzipped fasta file | 1 sec | Passed |
| saveAsParquet with file path | 0.49 sec | Passed |
| saveAsParquet with file path, block size, page size | 0.96 sec | Passed |
| saveAsParquet with save args | 0.41 sec | Passed |
| sc.loadParquet should not fail on unmapped reads | 0.24 sec | Passed |
| sc.loadParquet should not load a file without a type specified | 0.43 sec | Passed |
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