Test Result : AlignmentDatasetSuite

0 failures (±0) , 1 skipped (±0)
107 tests (±0)
Took 3 min 57 sec.

All Tests

Test nameDurationStatus
GenomicDataset.sort does not fail on unmapped reads1.1 secPassed
GenomicDataset.sortLexicographically does not fail on unmapped reads0.17 secPassed
SAM conversion sets read mapped flag properly0.12 secPassed
bin quality scores in reads1.1 secPassed
binning quality scores in reads succeeds even if reads have no quality scores0.17 secPassed
can properly set environment variables inside of a pipe1.4 secPassed
cannot have a null processing step ID1 msPassed
cannot provide bins with a gap90 msPassed
cannot provide empty quality score bins95 msPassed
cannot provide overlapping bins0.49 secPassed
computes coverage8.9 secPassed
computes coverage with multiple samples2 secPassed
convert a processing description to htsjdk0 msPassed
convert alignments to reads0.22 secPassed
convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM5.5 secPassed
coverage does not fail on unmapped reads0.47 secPassed
don't lose any reads when piping as BAM1.4 secPassed
don't lose any reads when piping as SAM1.5 secPassed
don't lose any reads when piping as SAM using java pipe1.5 secPassed
don't lose any reads when piping fastq to sam1.8 secPassed
filter RDD bound alignments by MAPQ0.88 secPassed
filter RDD bound alignments to primary alignments0.11 secPassed
filter RDD bound alignments to read group0.12 secPassed
filter RDD bound alignments to read groups0.77 secPassed
filter RDD bound alignments to sample1.2 secPassed
filter RDD bound alignments to samples0.87 secPassed
filter RDD bound duplicate alignments0.1 secPassed
filter RDD bound unaligned alignments1.1 secPassed
filter RDD bound unpaired alignments1.1 secPassed
filter dataset bound alignments by MAPQ0.22 secPassed
filter dataset bound alignments to primary alignments1 secPassed
filter dataset bound alignments to read group1 secPassed
filter dataset bound alignments to read groups0.25 secPassed
filter dataset bound alignments to sample0.99 secPassed
filter dataset bound alignments to samples1.4 secPassed
filter dataset bound duplicate alignments0.62 secPassed
filter dataset bound unaligned alignments0.22 secPassed
filter dataset bound unpaired alignments1.3 secPassed
left normalize indels0.11 secPassed
load FASTQ with no bases0.52 secPassed
load from sam, save as partitioned parquet, and re-read from partitioned parquet9.7 secPassed
load long FASTQ reads0.77 secPassed
load parquet to sql, save, re-read from avro8.5 secPassed
lose all records when a command times out11 secPassed
lose no records without a timeout11 secPassed
lose some records when a command times out11 secPassed
merges adjacent records with equal coverage values0.55 secPassed
read vcf from alignment pipe0 msSkipped
round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values2 secPassed
round trip from ADAM to SAM and back to ADAM produces equivalent Read values1.2 secPassed
round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values6 secPassed
round trip with sharded CRAM file produces equivalent Read values2.1 secPassed
round trip with single CRAM file produces equivalent Read values3.6 secPassed
running base recalibration with downsampling doesn't drop reads8.1 secPassed
save as ADAM parquet format0.19 secPassed
save as BAM format1.5 secPassed
save as FASTQ format0.98 secPassed
save as SAM format0.45 secPassed
save as sorted BAM format0.83 secPassed
save as sorted SAM format0.18 secPassed
saveAsFastq0.98 secPassed
saveAsFastq as single file1.8 secPassed
saveAsFastq paired FASTQ3.1 secPassed
saveAsFastq sorted by read name0.51 secPassed
saveAsFastq sorted by read name with original base qualities0.95 secPassed
saveAsFastq with original base qualities0.16 secPassed
saveAsPairedFastq1.4 secPassed
saveAsPairedFastq as single files2.8 secPassed
saveAsParquet with save args, sequence dictionary, and read group dictionary2.9 secPassed
saveAsSam BAM format0.17 secPassed
saveAsSam BAM format single file0.55 secPassed
saveAsSam SAM format0.55 secPassed
saveAsSam SAM format single file1.2 secPassed
saveAsSam sorted BAM format single file0.98 secPassed
saveAsSam sorted SAM format single file1 secPassed
sort by read name2.1 secPassed
sorting reads5 secPassed
sorting reads by reference index1 secPassed
test dataset based k-mer counter6.3 secPassed
test k-mer counter1.2 secPassed
transform dataset via java API1.3 secPassed
transform reads to coverage genomic dataset1.7 secPassed
transform reads to feature genomic dataset1.5 secPassed
transform reads to fragment genomic dataset3 secPassed
transform reads to genotype genomic dataset2.2 secPassed
transform reads to slice genomic dataset1.7 secPassed
transform reads to variant genomic dataset2.8 secPassed
union two read files together1.2 secPassed
unmapped reads go at the end when sorting0.44 secPassed
use broadcast join against to pull down reads mapped to targets3.5 secPassed
use broadcast join to pull down reads mapped to targets3.8 secPassed
use full outer shuffle join to pull down reads mapped to targets4.8 secPassed
use left outer shuffle join to pull down reads mapped to targets4 secPassed
use right outer broadcast join against to pull down reads mapped to targets2.6 secPassed
use right outer broadcast join to pull down reads mapped to targets2.8 secPassed
use right outer shuffle join to pull down reads mapped to targets3.1 secPassed
use right outer shuffle join with group by to pull down reads mapped to targets3.8 secPassed
use shuffle join to pull down reads mapped to targets3.9 secPassed
use shuffle join with feature spanning partitions3.2 secPassed
use shuffle join with flankSize to pull down reads mapped close to targets3.7 secPassed
use shuffle join with group by to pull down reads mapped to targets2.7 secPassed
write single bam file back6.2 secPassed
write single sam file back6.5 secPassed
writing a small file with tags should produce the expected result2.5 secPassed
writing a small sorted file as SAM should produce the expected result0.49 secPassed
writing ordered sam from unordered sam1.9 secPassed
writing unordered sam from unordered sam1.6 secPassed