Confirm alignment

[Nicklas Nordborg]

Confirmation is needed after the filter/alignment step. The normal workflow is to continue with Cufflinks, but it should be possible to mark as not successful and flag the RNA or redo the alignment (eg. due to some temporary software failure).

More details will follow during the implementation...

[Nicklas Nordborg]

(In [2404]) References #595: Confirm alignment

First version of the wizard. It lists all finished filter/align jobs. It is possible to select among three outcomes (multiple options can be selected):

• Flag RNA
• Re-align
• Cufflinks

[Nicklas Nordborg]

(In [2406]) References #595: Confirm alignment

Adding a function for listing and downloading files that was generated in the filter/align step.

[Nicklas Nordborg]

(In [2407]) References #595: Confirm alignment

Extended the file listing feature with a function for copying result files to the BASE file system.

[Nicklas Nordborg]

(In [2417]) References #595: Confirm alignment

Saved files are attached to the aligned derived bioassay using AnyToAny links.

[Nicklas Nordborg]

(In [2420]) References #533, #547, #548, #593, #595. Renamed FilteredSequences subtype to MaskedSequences and the related software and protocol type. Renamed annotations NumReads to READS and PassedFilterReads to PF_READS and added new annotation for number of reads on the masked (PM_READS) and aligned level (ALIGNED_PAIRS).

Lots of related changes in the code to make class and variable names match the new names.

[Nicklas Nordborg]

(In [2499]) References #595: Confirm alignment

Display PT_READS in the confirmation wizard.

[Nicklas Nordborg]

(In [2573]) References #595: Confirm alignment

Changes related to [2566] due to paths now being stored with a starting '/'.

[Nicklas Nordborg]

(In [2574]) References #595: Confirm alignment

Better progress reporting during file transfer. Improved performance of file transfer by using a BufferedInputStream.

[Nicklas Nordborg]

(In [2575]) References #595: Confirm alignment

Do not need to open 2 DbControl:s.

[Nicklas Nordborg]

(In [2578]) References #595: Confirm alignment

Linkf generated files with the 'AlignedSequences' bioassay. The 'accepted_hits.bam' is linked as a data file, all other files are linked as any-to-any links.

Removed the functionality to transfer the files to BASE.

[Nicklas Nordborg]

(In [2633]) References #593 and #595. Added "delete items created by failed jobs" option to alignment confirmation wizard.

This will delete MaskedSequences and AlignedSequences items so that the database is not filled up with unintersting items.

Re-starting the alignment will create new items with the same names so the script sent to the cluster has been modified so that it makes sure that the folders it is going to use are empty before starting to add data to them. Eg:

mkdir -p folder
rm -rf folder/*

[Nicklas Nordborg]

(In [2635]) References #593 and #595. Changes in [2633] that ensure job folders are empty also deleted sample sheet files uploaded by the demux script. The job definition has been modified so that files that are needed by the job must be part of the definition and uploaded at the same time as the job is sent to the cluster.

[Nicklas Nordborg]

(In [2638]) References #595: Confirm alignment

Do not show the 'delete items created by failed jobs' option if there are no failed jobs.

[Nicklas Nordborg]

(In [2644]) References #595: Confirm alignment

The 'View remote files' dialog now uses reggie-2.js and reggie-2.css.

[Nicklas Nordborg]

(In [2685]) References #595: Confirm alignment

Same change as [2683] for the demux confirmation wizard:

• Also delete file items linked with bioassays if the "delete items" option is selected.
• Made the import of files more robust by allowing it to overwrite existing files.

[Nicklas Nordborg]

(In [2706]) References #593 and #595. Parse 'accepted_hits_picardmetrics.csv' and read out three values:

• READ_PAIRS_EXAMINED
• READ_PAIR_DUPLICATES
• PERCENT_DUPLICATION (FRACTION_DUPLICATION)

The values are stored in annotations on the AlignedSequences item. Note that what Picard says is a percentage is actually a fraction.