Extensive IGV Name Parameter #316
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Reviewing... |
| * Ref: https://umccr.slack.com/archives/CP356DDCH/p1707116441928299?thread_ts=1706583808.733149&cid=CP356DDCH | ||
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| * The desired outcome is to include libraryId, sampleId, type, and filetype | ||
| * Desired output: SBJ00000_WGS_L0000000_PRJ00000_tumor.bam |
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Oh, sorry Will. Spec change a bit. Could you remove sample type field, pls?
It should just be the SubjectID_LibraryID_ prepending only.
e.g. SBJ00000_L0000000_PRJ00000_tumor.bam
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Sorry just thought I could go for an extra mile here to include the type. But, yes could follow what we agree on slack. Changing it ...
| indexed: false, | ||
| visibilityWindow: -1, | ||
| removable: false, | ||
| order: 1000000, | ||
| infoURL: 'https://www.ncbi.nlm.nih.gov/gene/?term=$$', |
| nameArray.push(...findMatchingProperty('library_id')); | ||
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| // 3. sampleId + filetype | ||
| nameArray.push(pathOrKey.split('/').pop() ?? pathOrKey); |
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I'd like to discuss the logic a little bit here. Perhaps, we catchup tomorrow.
Especially for BAM case, we might not want to match library_id from the path. The path pertaining two library_id has other meaning as they belong to a single workflow run.
However, a BAM file only represents 1 sample; either tumor or normal. So, we need to extract sample_id from the filename; strip tumor or normal (if exists); then using this sample_id to exchange its library_id counterpart from the subject meta/lims. So it is to be precise. It will be rather filter (or lookup) logic than reducing with accumulator on all possible library_id matches infer from the path.
What you did here is; arguable not completely wrong either - especially when we switch to VCF context. But then, that open up even more complex handling where I'd rather ignore prefix for VCF all together. Only support BAM case.
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I made the change so only bam that will have the SBJ00000_L0000000_PRJ00000_tumor.bam format while other filetype will only prepend the subjectId
{subjectId}_{type}_{libraryId}_filename.bamfor both IGV local and jsRef: Slack - Threads