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  • Issue 1: Samples marked WXS/WGS in the gene panel matrix file but do not exist in the sequenced case list -> TMB = 0.0 (should be NA)
  • Issue 2: Gene panel matrix file has value "NA" for panel ID -> KeyError

Fixes:

  • "NA" is an accepted value in the gene panel matrix file
  • Samples that exist in sequenced case list and have an "NA" in the gene panel matrix file will have TMB computed
  • Samples in the gene panel matrix file with any value (WXS/WGS) but not present in the sequenced case list are not sequenced and so get "NA" for TMB instead of 0

Comment on lines +131 to +139
# assign CDS value, use 'NA' if panel ID is missing or invalid
if _panelID in ["NA", "", "None"] or _panelID not in _cdsMap:
_cds = "NA"
else:
_cds = _cdsMap[_panelID]

# If sample is sequenced but CDS is NA, assign default WES/WGS CDS
if _cds == "NA" and _sampleID in _seqSampleIds:
_cds = WES_WGS_CDS
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Getting a TabError: inconsistent use of tabs and spaces in indentation

if _panelID in ["NA", "", "None"] or _panelID not in _cdsMap:
_cds = "NA"
else:
_cds = _cdsMap[_panelID]
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IndentationError: expected an indented block after 'else' statement

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3 participants