# Conflicts:
#	public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
#	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
#	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
#	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
#	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
#	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

Feature report

second phase for reporting

Adding report to all general pipelines

See merge request !184

Issue164

See #164

See merge request !186

Fix the test of seqstat, so that develop can build again

See merge request !188

Conflicts:
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

Working dir for unit tests is now the target folder

Fix for #150

See merge request !176

Small fixes

Fixes two small issues

1. Extra docs for target beds/regions of interest for Shiva
2. Fixes integer overflow on WGS coverage statistics for report (Size of human genome > 2^31 -1 bases)

See merge request !177

Patch picard dependency list

This pull request deals with a recent change in pulling Picard's version number. Previously, the version number is generated only when the JAR is packaged. This means if we do `mvn test` or run tests on specific classes directly, we'll get `NullPointerException` since the dependency list is not created yet.

To fix this, the pulled dependency list stream is wrapped properly in an `Option` class now (so we can run tests directly on classes).

See merge request !180

Feature gentrap additions

This is the latest updates and fixes on the Gentrap pipeline to be compatible with the most recent framework updates.

In particular:

* Issue #156 is fixed ~ this was due to class initialization problems
* Issue #157 is fixed
* TopHat alignment results are now merged with its unmapped alignment file, producing the correct statistics
* The pipeline is updated with the new reference module.
* Redundant CollectRnaSeqMetrics is removed (now using the one from BamMetrics instead).

See merge request !181

Feature seqstat updates

Updates on SeqStat (per the commit messages).

We still need to rely on FastQC since some other methods require further testing to be implemented. For example, to get the median base quality from all bases is not that straightforward since the container size may well exceet `Int.MaxValue` while the default containers' maximum sizes are all `Int.MaxValue`.

See merge request !182

Shiva report messages

Add messsages for Shiva report

See #168

See merge request !183

Feature fix java version

Fix for #144

See merge request !185