VET Ingest Validation / Allow Ingest of non-VQSR'ed data #7870
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -30,12 +30,12 @@ | |
| * location, // req | ||
| * reference_bases, // req | ||
| * alternate_bases_alt, // req | ||
| * alternate_bases_AS_RAW_MQ, | ||
| * alternate_bases_AS_RAW_MQRankSum, | ||
| * alternate_bases_AS_QUALapprox, | ||
| * alternate_bases_AS_RAW_ReadPosRankSum, | ||
| * alternate_bases_AS_SB_TABLE, | ||
| * alternate_bases_AS_VarDP, | ||
| * call_genotype, // req | ||
| * call_AD, | ||
| * call_DP, // Laura says consider removing for now-- so similar to AS_VarDP | ||
|
|
@@ -76,7 +76,7 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| }, | ||
|
|
||
| AS_RAW_MQ { | ||
| // Required for VQSR Data | ||
| // can strip off the first one? | ||
| // TODO sci notation? | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
|
|
@@ -87,10 +87,10 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| throw new UserException("Cannot be missing required value for alternate_bases.AS_RAW_MQ, RAW_MQandDP or RAW_MQ."); | ||
| } | ||
| if (!forceLoadingFromNonAlleleSpecific && out != null) { | ||
| // KC: we are seeing a TON of these! | ||
| // if (!out.endsWith("|0.00")) { | ||
|
There was a problem hiding this comment. Yeah, @kcibul commented out the logger statement, I just expanded the commenting out to take out all the functional code. |
||
| // logger.warn("Expected AS_RAW_MQ value to end in |0.00. value is: " + out + " for variant " + variant.toString()); | ||
| // } | ||
| out = out.substring(0, out.lastIndexOf("|")); | ||
| String[] outValues = out.split("\\|"); | ||
| out = Arrays | ||
|
|
@@ -124,9 +124,13 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| return outNotAlleleSpecific; | ||
| } | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| AS_RAW_MQRankSum { // TODO -- maybe rely on 1/1 for call_GT, also get rid of the | at the beginning | ||
| // Required for VQSR Data | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| // in the case where neither allele is reference, don't return a value | ||
| if (isGenotypeAllNonRef(variant.getGenotype(0))) { | ||
|
|
@@ -175,27 +179,34 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| //throw new UserException("Expected AS_RAW_MQRankSum value to be ||, ||| or to end in |NaN"); | ||
| } | ||
| return out; | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| QUALapprox { | ||
| // Required for VQSR Data | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| String out = getAttribute(variant, RAW_QUAL_APPROX_KEY, null); | ||
| if (out == null) { | ||
| throw new UserException("Cannot be missing required value for QUALapprox at site: " + variant); | ||
| } | ||
| return out; | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| AS_QUALapprox { | ||
| // Required for VQSR Data | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| String out = getAttribute(variant, AS_RAW_QUAL_APPROX_KEY, null); | ||
| if (out == null) { | ||
| String outNotAlleleSpecific = getAttribute(variant, RAW_QUAL_APPROX_KEY, null); | ||
| if (outNotAlleleSpecific == null) { | ||
| throw new UserException("Cannot be missing required value for AS_QUALapprox or QUALapprox at site: " + variant); | ||
| } | ||
| return outNotAlleleSpecific; | ||
| } | ||
|
|
@@ -217,6 +228,9 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| } | ||
| return out; | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| AS_RAW_ReadPosRankSum { // TODO -- maybe rely on 1/1 for call_GT | ||
|
|
@@ -268,9 +282,13 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| } | ||
| return out; | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| AS_SB_TABLE { | ||
| // Required for VQSR Data | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| String out = getAttribute(variant, GATKVCFConstants.AS_SB_TABLE_KEY, null); | ||
| if (forceLoadingFromNonAlleleSpecific || out == null) { | ||
|
|
@@ -296,16 +314,20 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| } | ||
| return out; | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| AS_VarDP { | ||
| // Required for VQSR Data | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| String out = getAttribute(variant, AS_VARIANT_DEPTH_KEY, null); | ||
| if (out == null) { | ||
| String varDP = getAttribute(variant, VARIANT_DEPTH_KEY, null); | ||
| String dP = getAttribute(variant, DEPTH_KEY, null); | ||
| if (varDP == null || dP == null) { | ||
| throw new UserException("Cannot be missing required value for AS_VarDP, or VarDP and DP, at site:" + variant); | ||
| } | ||
| int refDP = Integer.parseInt(dP) - Integer.parseInt(varDP); | ||
| out = refDP + "|" + varDP + "|"; | ||
|
|
@@ -319,10 +341,16 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| } | ||
| return out; | ||
| } | ||
| public boolean isVqsrSpecificField() { | ||
| return true; | ||
| } | ||
| }, | ||
|
|
||
| call_GT { | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| if (!variant.hasGenotypes()) { | ||
| throw new UserException("Cannot be missing required value for call.GT"); | ||
| } | ||
| // TODO how is missing handled? | ||
| return CommonCode.getGTString(variant); | ||
| } | ||
|
|
@@ -357,8 +385,7 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| call_GQ { // Required | ||
| public String getColumnValue(final VariantContext variant, final boolean forceLoadingFromNonAlleleSpecific) { | ||
| if (!variant.getGenotype(0).hasGQ()) { | ||
| throw new UserException("Cannot be missing required value for call.GQ"); | ||
| } | ||
| return String.valueOf(variant.getGenotype(0).getGQ()); | ||
| } | ||
|
|
@@ -389,6 +416,10 @@ public String getColumnValue(final VariantContext variant, final boolean forceLo | |
| throw new IllegalArgumentException("Not implemented"); | ||
| } | ||
|
|
||
| public boolean isVqsrSpecificField() { | ||
| return false; | ||
| } | ||
|
|
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| public static boolean isGenotypeAllNonRef(Genotype g) { | ||
| return g.getAllele(0).isNonReference() && g.getAllele(1).isNonReference(); | ||
| } | ||
|
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||
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This addresses VS-455