bigdatagenomics / quinine

A refreshing treatment for all quality control ailments. Apache 2 licensed.

quinine: A refreshing treatment for all quality control ailments

Read and variant metrics, useable for pipeline quality control purposes

quinine's Issues

Add sample contamination estimator

Update ADAM and plugin dependency versions

Upgrade to ADAM 0.20.0

• Revert a0d455b
• Revert a5cb6b0
• Revert e47e7f4

Add MAF annotator

Necessary for running the contamination estimator from #19

Use flanking instead of startEnd

Minor doc issue here, might be worth using "flanking" instead of "startEnd" here and elsewhere

https://github.com/bigdatagenomics/quinine/blob/master/quinine-core/src/main/scala/org/bdgenomics/quinine/metrics/rna/RNASeqPanelStats.scala#L39

ReadStats NPE's on reads with null qualities

If you run on reads with * qualities, you get:

Command body threw exception:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost): java.lang.NullPointerException
        at scala.collection.immutable.StringOps$.length$extension(StringOps.scala:49)
        at scala.collection.immutable.StringOps.length(StringOps.scala:49)
        at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:32)
        at scala.collection.immutable.StringOps.foreach(StringOps.scala:31)
        at scala.collection.TraversableOnce$class.count(TraversableOnce.scala:113)
        at scala.collection.immutable.StringOps.count(StringOps.scala:31)
        at org.bdgenomics.quinine.metrics.targeted.ReadStats$.apply(ReadStats.scala:204)
        at org.bdgenomics.quinine.metrics.targeted.ReadStats$$anonfun$apply$1.apply(ReadStats.scala:253)
        at org.bdgenomics.quinine.metrics.targeted.ReadStats$$anonfun$apply$1.apply(ReadStats.scala:253)

Scoverage plugin not used properly

The same problem as bigdatagenomics/utils#95

Register your spark package

You have a dependency on Apache Spark. You can register your package at
http://spark-packages.org/register.
It's "[a] community index of packages for Apache Spark."

Provide separate artifacts for scala 2.10/2.11

Cross compiling for scala 2.10/2.11 is already supported with the scripts/move_to_scala_2.x scripts; a release script similar to

https://github.com/bigdatagenomics/adam/blob/master/scripts/release/release.sh

should be added.

Load allele frequencies from annotated VCFs

Filter out unmapped reads before running Region Joins

Add in metrics for targeted sequencing panels

A la HsMetrics.

Add Sequence Ontology identifiers as supported featureTypes

E.g. here
https://github.com/bigdatagenomics/quinine/blob/master/quinine-core/src/main/scala/org/bdgenomics/quinine/metrics/rna/RNASeqAlignmentCounts.scala#L43

Check if mate is aligned before creating mate ReferenceRegion

https://github.com/bigdatagenomics/quinine/blob/master/quinine-core/src/main/scala/org/bdgenomics/quinine/metrics/targeted/ReadStats.scala#L214

Add RNA-seq QC tool

A la RNA-seQC.

Check collection size in contamination estimator before running

RDD should not be empty. If it is, then we get an empty reduce by. We should warn if we get an empty RDD.

Compute insert size distribution

See bigdatagenomics/adam#296

Join on variant in contamination estimator is flaky

https://github.com/bigdatagenomics/quinine/blob/master/quinine-core/src/main/scala/org/bdgenomics/quinine/metrics/contamination/VariantSite.scala#L63

Contamination estimator can fail if 95% window is too small

If there are no points in the 95% confidence window, we can minBy/maxBy on an empty collection.

`CoverageStats` trips assert if distribution is empty

This assert fires: https://github.com/bigdatagenomics/quinine/blob/master/quinine-core/src/main/scala/org/bdgenomics/quinine/metrics/coverage/CoverageStats.scala#L114

String index out of range in ContaminationEstimator/VariantSite

Vote of no confidence in new repository name

Release a v0.0.1

We have some things in Guacamole that depend on this and it's a little awkward to have to just point at the Maven snapshot that is the only artifact that exists, afaict.

Package names are wrong...

The packages are org.bdgenomics.adam

Compute coverage distribution

See bigdatagenomics/adam#1010