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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Keep presence of alignment and assembly report fields consistent #268

Closed joltex closed 6 years ago

joltex commented 6 years ago

Sometimes certain alignment and assembly report fields are missing. For example, "Alignment failed because of low total score" appears for some samples or sequencing runs but not for others. I assume this is because some samples have no reads failing alignment for this reason - they might be MiGEC / high quality reads for example.

This makes summarizing multiple samples or sequencing runs more troublesome. It would be better to always show these fields and give a value of '0' if the given sample had no reads falling into the given category.

dbolotin commented 6 years ago

Sorry for delayed response. Agree! We will add JSON report output option. In this case, it will be even possible to quick-summarise results with util like jq. Will it solve the problem for you?

joltex commented 6 years ago

Yes, I think a JSON report would be great. I generally parse all the individual report files for a sequencing run of many samples to generate a single report table.

dbolotin commented 6 years ago

Good! The plan now is to implement each report as single line JSON (like described here), so you can specify the same file in several mixcr invocations, and each subsequent report will be added to it line by line.