Conflicts:
	.idea/compiler.xml
	.idea/encodings.xml
	.idea/misc.xml
	.idea/modules.xml
	.idea/scala_compiler.xml
	.idea/vcs.xml
	protected/basty/Basty.iml
	protected/biopet-gatk-extensions/BiopetGatkExtensions.iml
	protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml
	protected/biopet-protected-package/BiopetProtectedPackage.iml
	public/bammetrics/BamMetrics.iml
	public/biopet-framework/BiopetFramework.iml
	public/biopet-public-package/BiopetPublicPackage.iml
	public/flexiprep/Flexiprep.iml
	public/gentrap/Gentrap.iml
	public/mapping/Mapping.iml
	public/sage/Sage.iml
	public/yamsvp/Yamsvp.iml

Patch flagstat dirs

This fixes the recent update of `ouputDir` from `String` to `File`. There are some `apply` method that are overloaded with both `String` and `File`, causing the pipeline to spew out weird error messages.

@p.j.van_t_hof ~ this is what was causing the weird error earlier.

See merge request !101

Patch ide files

This patch excludes existing IDE-specific files from the git index. I'm not sure yet if this solution works clean for everybody, so please test it first locally.

@wyleung & @p.j.van_t_hof , this is what we discussed earlier with the `*.iml` files and `.idea/*` files.

See merge request !98

Patch develop defaultvmem

patch

See merge request !97

Patch pipelines test

This is a patch for the newly added pipeline tests to ensure that each pipeline test has a unique directory that is removed after the test. The curren behaviour is to use a named directory in the user's tmp directory, that may fail if a directory with that name already exist.

@p.j.van_t_hof , this is what we discussed earlier.

See merge request !96

Patch fastq sync stream

The current implementation of `FastqSync` creates an intermediate Stream that is then passed to a writing function. Apparently, the `Stream` is not evaluated as lazily (or not in the way) as I thought. This led to weird StackOverflow errors (not yet documented).

This fix merges the Stream creation and writing function, so that no intermediate containers are created and no errors are encountered. Tests have been updated accordingly.

See merge request !95

Patch coniferfix

There was a bug in reading files from the RPKM ref directory.

Now filters to *.txt and the .out file is now created as a hidden file (for inprocess runs we need to overrride this)

Reporter: Gijs Santen,
Fix: Wai Yi Leung

See merge request !93

Flexiprep unit test + fix for small bugs

See subject

See merge request !94

Conflicts:
	protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
	public/mapping/pom.xml