Add masking step to Hisat pipeline

[Nicklas Nordborg]

The same masking that is done in the legacy pipeline before Tophat is run should also be done in the Hisat pipeline.

This means that we need to re-introduce the MaskedSequences item. Statistics should be imported to the PM_READS annotation.

[Nicklas Nordborg]

(In [4656]) References #1015: Add masking step to Hisat pipeline

The masking is step is now included in the job script.

Software and protocol parameters are selected from the project default (NOT using the Tophat vs. Hisat setting since we use the same in both pipelines).

A MaskedSequences item is created and the PM_READS annotions is populated with information from the mask step.

There are still some places in the code that may be "suprised" by the masked parent item (causing a NPE). This needs to be fixed.

The Hisat confirmation wizard should also display the PM_READS annotation.

[Nicklas Nordborg]

(In [4657]) Fixes #1015: Add masking step to Hisat pipeline

The PM_READS annotation is now displayed in the confirmation wizard.

Deprecated the AlignedSequences.getMergedSequences() method. This should be removed once we have deleted all alignments without a masking step from the database.

[Nicklas Nordborg]

(In [4676]) References #1018 and #1015.

Adding "reads after mask" and HET percentage to the final job status report. Changed the duplication percentage to only use one decimal (also done in the legacy pipeline).

[Nicklas Nordborg]

(In [4680]) References #1015: Add masking step to Hisat pipeline

Added a wizard for deleting existing Hisat alignments that doesn't have a masking step. This should make it easier to delete all linked files and directories. Files on the file server should be deleted with the "Stray files wizard".