Import some information from filtering-stats.txt

[Nicklas Nordborg]

The WGS variant calling pipeline creates a file filtering-stats.txt with some information about the filtering step (FilterMutectCalls). We should import some of this to annotations:

• From the METADATA section: fdr and sensitivity
• From the table: Sum of FP and FN (False positives/negatives)

[Nicklas Nordborg]

In 7482:

References #1551: Import some information from filtering-stats.txt

The filtering-stats.txt file is now parsed and values are added to the metrics instance.

[Nicklas Nordborg]

In 7483:

References #1551: Import some information from filtering-stats.txt

Created 4 new annotation types for saving the values from filtering-stats.txt.

[Nicklas Nordborg]

In 7484:

References #1551: Import some information from filtering-stats.txt

Display some of the statistics information in the confirmation wizard and in the "View variants" dialog.

[Nicklas Nordborg]

In 7486:

References #1551: Import some information from filtering-stats.txt

Added 'FDR' and 'Sensitivity' to the case summary. Display value as percentages instead of fractions.

[Nicklas Nordborg]

In 7487:

References #1543: Release exporter changes due to WGS data

Include new annotations from the filter-stats.txt (see #1551) file in the release data.

[Nicklas Nordborg]

In 7495:

References #1551: Import some information from filtering-stats.txt

Use percentage in the final message on the job item.