bigdatagenomics / adam / 4162 / 1

Ran 10 Feb 2019 08:11AM CUT

Files 142

Run time 7s

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Committed 10 Feb 2019 08:11AM CUT coverage: 79.075%. Remained the same

Job # 4162.1

Build Type

push

jenkins

Committed by Michael L Heuer

Commit Message

Filter supplemental reads from scoring

Currently a supplemental read can be added to the sum of base qualities
of a duplicate candidate, artificially inflating its base quality sum
when mark duplicates is trying to choose the best read from the bunch.

This is one (the simplest and most superficial) fix to the problem. Just
filter supplemental reads out when summing.

Another solution could be to use the supplemental flag when setting the
"not primary read flag" in SAMRecordConverter.

Yet another would be to create a separate field in SingleReadBucket for
supplemental reads.

Not sure what the downstream effects of these different approaches are.

Run Details

6738 of 8521 relevant lines covered (79.08%)

0.79 hits per line

Source Files on job 4162.1

Coverage	File	Lines	Relevant	Covered	Missed	Hits/Line
0.0	...dgenomics/adam/api/java/GenomicRDDConverters.scala	485 + 393	64 + 29	0 - 34	64 + 63	0.0 - 1.0
0.0	...scala/org/bdgenomics/adam/util/ParquetLogger.scala	35 - 11	2 - 24	0 - 24	2	0.0 - 1.0
0.0	...org/bdgenomics/adam/rdd/ReferencePartitioner.scala	58 - 12	7 - 23	0 - 2	7 - 21	0.0 - 1.0
0.0	...ain/scala/org/bdgenomics/adam/util/ADAMShell.scala	384 - 35	143 - 81	0 - 216	143 + 135	0.0 - 1.0
0.0	...omics/adam/api/java/GenomicDatasetConverters.scala	381 + 340	50 + 28	0 - 19	50 + 47	0.0 - 1.0
0.0	.../bdgenomics/adam/util/ParquetFileTraversable.scala	86 + 66	23 + 10	0 - 12	23 + 22	0.0 - 1.0
0.0	...s/adam/api/python/DataFrameConversionWrapper.scala	30 - 29	1 - 33	0 - 29	1 - 4	0.0 - 1.0
0.0	...onsensus/ConsensusGeneratorFromSmithWaterman.scala	92 + 63	15 - 9	0 - 23	15 + 14	0.0 - 1.0
3.28	.../main/scala/org/bdgenomics/adam/cli/FlagStat.scala	140 + 124	61 + 53	2 - 6	59 + 59	1.0
5.88	...ain/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala	96 - 14	34 - 39	2 - 67	32 + 28	1.0

7.46
adam-apis/
57.38
adam-cli/
82.36
adam-core/

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