Updates to registration of specimen handled by external lab

[Nicklas Nordborg]

See #1295 for background.

New features:

• R1size and R2size entries in the fastq section that can be used to verify that the complete FASTQ files have been transfered.

• Library/Plate well entry is now specifying coordinates using A:1 format. Update It was not just a formatting issue. The 'A:1' format is used when the library prep is made on 8x12 plates and the '1:1' format is used when the library prep is made on 1x8 strips. The plate format is going to be used in the normal workflow, but there may be situations when the strip format is used instead. We should model this and introduce a "LibStrip?" plate type with 1x8 geometry. We can use the format of the Library/Plate well value to decide which plate type to use.

• New value in Library/Protocol: TruSeq Stranded mRNA - Expression - Breast. The ExternalRef annotation for the corresponding library protocol need to be updated manually in lorry.

[Nicklas Nordborg]

In 6457:

References #1347: Updates to registration of specimen handled by external lab

Implemented support for checking FASTQ file size.

[Nicklas Nordborg]

In 6458:

References #1347: Updates to registration of specimen handled by external lab

Fixes a NullPointerException if the SCANB_ID entry is missing.

[Nicklas Nordborg]

In 6459:

References #1347: Updates to registration of specimen handled by external lab

The changes in [6457] and [6458] was committed to the trunk but they should have been in the reggie/4.33-stable branch. This update merge the same changes to the reggie/4.33-stable
branch.

[Nicklas Nordborg]

In 6460:

References #1347: Updates to registration of specimen handled by external lab

Added support for plate coordinates in "A:1" format.

[Nicklas Nordborg]

In 6462:

References #1347: Updates to registration of specimen handled by external lab

Added a column for showing the number of reads in the FASTQ files.

[Nicklas Nordborg]

In 6463:

References #1347: Updates to registration of specimen handled by external lab

Increasing the warning limit about library size to 500.

[Nicklas Nordborg]

In 6464:

References #1347: Updates to registration of specimen handled by external lab

Added new plate type "External library strip" and new geometry "1x8".

[Nicklas Nordborg]

In 6465:

References #1347: Updates to registration of specimen handled by external lab

The library importer will now select the plate type depending on the format of the Plate well value. If the value is digit:digit the STRIP_1x8 is selected otherwise the PLATE_8x12.

[Nicklas Nordborg]

In 6466:

References #1347: Updates to registration of specimen handled by external lab

Make the FASTQ file size easer to read by using a thousands separator.

[Nicklas Nordborg]

In 6467:

References #1347: Updates to registration of specimen handled by external lab

Figure out which FASTQ is R1 and which is R2 by checking the stored annotation values instead of using the find command. The pattern used may not always match.

[Nicklas Nordborg]

In 6468:

References #1347: Updates to registration of specimen handled by external lab

Use the number of reads in the FASTQ files to set the READS annotation.

[Nicklas Nordborg]

In 6469:

References #1347: Updates to registration of specimen handled by external lab

Changing the soft warning limits for the number of reads and improving the display by adding thousand separators.