Test Result : AlignmentDatasetSuite

0 failures (±0) , 1 skipped (±0)
107 tests (±0)
Took 2 min 6 sec.

All Tests

Test nameDurationStatus
GenomicDataset.sort does not fail on unmapped reads0.5 secPassed
GenomicDataset.sortLexicographically does not fail on unmapped reads0.66 secPassed
SAM conversion sets read mapped flag properly0.17 secPassed
bin quality scores in reads1.6 secPassed
binning quality scores in reads succeeds even if reads have no quality scores0.61 secPassed
can properly set environment variables inside of a pipe1.1 secPassed
cannot have a null processing step ID0 msPassed
cannot provide bins with a gap0.37 secPassed
cannot provide empty quality score bins0.24 secPassed
cannot provide overlapping bins0.33 secPassed
computes coverage1.4 secPassed
computes coverage with multiple samples2 secPassed
convert a processing description to htsjdk0 msPassed
convert alignments to reads0.41 secPassed
convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM0.56 secPassed
coverage does not fail on unmapped reads0.32 secPassed
don't lose any reads when piping as BAM0.41 secPassed
don't lose any reads when piping as SAM0.43 secPassed
don't lose any reads when piping as SAM using java pipe0.41 secPassed
don't lose any reads when piping fastq to sam0.96 secPassed
filter RDD bound alignments by MAPQ0.24 secPassed
filter RDD bound alignments to primary alignments0.17 secPassed
filter RDD bound alignments to read group0.22 secPassed
filter RDD bound alignments to read groups0.22 secPassed
filter RDD bound alignments to sample1 secPassed
filter RDD bound alignments to samples0.32 secPassed
filter RDD bound duplicate alignments0.17 secPassed
filter RDD bound unaligned alignments0.2 secPassed
filter RDD bound unpaired alignments0.29 secPassed
filter dataset bound alignments by MAPQ0.42 secPassed
filter dataset bound alignments to primary alignments0.38 secPassed
filter dataset bound alignments to read group0.4 secPassed
filter dataset bound alignments to read groups0.63 secPassed
filter dataset bound alignments to sample0.68 secPassed
filter dataset bound alignments to samples0.72 secPassed
filter dataset bound duplicate alignments0.35 secPassed
filter dataset bound unaligned alignments0.45 secPassed
filter dataset bound unpaired alignments0.68 secPassed
left normalize indels0.3 secPassed
load FASTQ with no bases0.45 secPassed
load from sam, save as partitioned parquet, and re-read from partitioned parquet2.2 secPassed
load long FASTQ reads0.26 secPassed
load parquet to sql, save, re-read from avro2.8 secPassed
lose all records when a command times out10 secPassed
lose no records without a timeout10 secPassed
lose some records when a command times out10 secPassed
merges adjacent records with equal coverage values1.2 secPassed
read vcf from alignment pipe0 msSkipped
round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values0.47 secPassed
round trip from ADAM to SAM and back to ADAM produces equivalent Read values0.56 secPassed
round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values1.7 secPassed
round trip with sharded CRAM file produces equivalent Read values0.54 secPassed
round trip with single CRAM file produces equivalent Read values0.58 secPassed
running base recalibration with downsampling doesn't drop reads6.8 secPassed
save as ADAM parquet format0.25 secPassed
save as BAM format0.24 secPassed
save as FASTQ format0.22 secPassed
save as SAM format0.23 secPassed
save as sorted BAM format0.26 secPassed
save as sorted SAM format0.22 secPassed
saveAsFastq0.24 secPassed
saveAsFastq as single file0.25 secPassed
saveAsFastq paired FASTQ1.1 secPassed
saveAsFastq sorted by read name0.35 secPassed
saveAsFastq sorted by read name with original base qualities0.34 secPassed
saveAsFastq with original base qualities0.24 secPassed
saveAsPairedFastq1.1 secPassed
saveAsPairedFastq as single files1.2 secPassed
saveAsParquet with save args, sequence dictionary, and read group dictionary0.47 secPassed
saveAsSam BAM format0.25 secPassed
saveAsSam BAM format single file0.3 secPassed
saveAsSam SAM format0.25 secPassed
saveAsSam SAM format single file0.3 secPassed
saveAsSam sorted BAM format single file0.26 secPassed
saveAsSam sorted SAM format single file0.26 secPassed
sort by read name1.4 secPassed
sorting reads0.83 secPassed
sorting reads by reference index0.87 secPassed
test dataset based k-mer counter4.7 secPassed
test k-mer counter0.6 secPassed
transform dataset via java API0.57 secPassed
transform reads to coverage genomic dataset1.2 secPassed
transform reads to feature genomic dataset1 secPassed
transform reads to fragment genomic dataset1.5 secPassed
transform reads to genotype genomic dataset2.5 secPassed
transform reads to slice genomic dataset1.9 secPassed
transform reads to variant genomic dataset1.7 secPassed
union two read files together0.8 secPassed
unmapped reads go at the end when sorting0.37 secPassed
use broadcast join against to pull down reads mapped to targets0.98 secPassed
use broadcast join to pull down reads mapped to targets1 secPassed
use full outer shuffle join to pull down reads mapped to targets2.6 secPassed
use left outer shuffle join to pull down reads mapped to targets3.2 secPassed
use right outer broadcast join against to pull down reads mapped to targets0.93 secPassed
use right outer broadcast join to pull down reads mapped to targets0.99 secPassed
use right outer shuffle join to pull down reads mapped to targets2 secPassed
use right outer shuffle join with group by to pull down reads mapped to targets2.7 secPassed
use shuffle join to pull down reads mapped to targets1.9 secPassed
use shuffle join with feature spanning partitions0.99 secPassed
use shuffle join with flankSize to pull down reads mapped close to targets1.7 secPassed
use shuffle join with group by to pull down reads mapped to targets2.9 secPassed
write single bam file back1.9 secPassed
write single sam file back1.9 secPassed
writing a small file with tags should produce the expected result0.46 secPassed
writing a small sorted file as SAM should produce the expected result0.38 secPassed
writing ordered sam from unordered sam0.41 secPassed
writing unordered sam from unordered sam0.23 secPassed