Combine two samples for HCV coverage

[donkirkby]

We don't have a single amplification that covers the whole HCV genome, so a patient will get two separate samples amplified with two projects: wg1HCV and MidHCV.
The MiSeq Monitor should identify these two samples by matching names, merge the two FASTQ files into one FASTQ file, and then process the merged file.
The QAI micall page should display some notes about which two samples were combined into each merged sample.

• identify pairs
• merge FASTQ's
• BaseSpace
• MiSeq monitor
• QAI notes
• quality control by trying to merge separate versions after analysis (separate issue?) Not relevant, because we didn't merge the FASTQ files.

[donkirkby]

We can't merge them in the FASTQ file, because there are rules about how to handle the overlapping section.
The current plan is to take the amino.csv files from the main pipeline, and combine them in a resistance analysis step that generates the reports.

[donkirkby]

I did this for the BaseSpace version as part of #412. It still needs to be done for the MiSeq monitor.

[donkirkby]

James is working on some changes to the QAI page, so we need to think about how to display the link between HCV and MidHCV samples. Perhaps they should be sorted next to each other, and displayed with a large curly brace to group them. That would echo the column groupings at the top.

When we add the review process, we'll have to generate resistance calls for all the samples, even the failed ones. That way, if a user overrides the failure, we can generate the final report.

It would be nice to show whether the report will be released or not on the QAI page. It's not clear whether a failure in unimportant regions will fail the report. I think we also talked about showing a sample summary by default, instead of the individual regions, but we'd have to discuss that with the users.

[donkirkby]

James has made the changes to QAI, and will release them soon. The MiCall changes for the review are in issue #439.
Closing this issue.