Release exporter changes due to WGS data

[Nicklas Nordborg]

We should include some WGS data in the next release. The starting point is existing BloodDNA (normal) and DNA (tumor) items that are already included in the release.

From the DNA items we go down to Library items. Extra aliquots inbetween are skipped.

From Library we skip the MergedSequences and go directly to AlignedSequences.

Then, we can add both CopyNumber items and VariantCall items as child items to the AlignedSequences items.

Relevant annotations should be included in the release. From library:

• Pipeline
• ExternalOperator

From alignments:

• Pipeline
• DataFilesFolder
• ALIGNED_BASES
• ALIGNED_PAIRS
• FRACTION_DUPLICATION
• FRACTION_OPTICAL_DUPLICATION
• FragmentSizeAvg
• FragmentSizeStdev
• MEAN_COVERAGE
• SD_COVERAGE
• PF_BASES
• PF_Q30_BASES
• QC_GenoTypeHET_PCT
• AlignmentSoftware

Files that should be included from alignments items:

• alignment.bam
• alignment.bai

From ASCAT items:

• Pipeline
• DataFilesFolder
• ImbalanceTest
• Penalty
• PsiManual
• RhoManual
• TauManual
• Ploidy
• Purity
• NormalContamination
• GoodnessOfFit
• GI_Score
• LOH_fraction
• NonAberrant

Files from ASCAT items:

• TODO