fixed bug; added tests #7717
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fixed bug; added tests #7717
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RoriCremer
reviewed
Mar 11, 2022
| @@ -128,14 +128,14 @@ public String getColumnValue(final VariantContext variant) { | |||
| // Try to use non-AS version | |||
| // TODO: it looks like the AS_RAW version also trims to a single decimal point?? | |||
| // e.g. MQRankSum=1.465 and turn it into |1.465,1| | |||
| String outNotAlleleSpecific = getAttribute(variant, GATKVCFConstants.READ_POS_RANK_SUM_KEY, null); | |||
| String outNotAlleleSpecific = getAttribute(variant, GATKVCFConstants.MAP_QUAL_RANK_SUM_KEY, null); | |||
RoriCremer
reviewed
Mar 11, 2022
| @@ -257,8 +257,8 @@ public String getColumnValue(final VariantContext variant) { | |||
| AS_SB_TABLE { // Required | |||
| public String getColumnValue(final VariantContext variant) { | |||
| String out = getAttribute(variant, GATKVCFConstants.AS_SB_TABLE_KEY, null); | |||
| String outNotAlleleSpecific = variant.getGenotype(0).getExtendedAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY, null).toString(); | |||
| if (out == null) { | |||
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what does this switch do?
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oh---was this a different bug?
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this was more that we were trying to parse out the "fallback" (non-AS) annotation even if we didn't need it. Now it just parses it if we can't find the first one. The tests caught it
RoriCremer
approved these changes
Mar 11, 2022
This was referenced Mar 17, 2023
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