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June 23, 2022 18:29
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| Exception reporting mode: Minimal | |
| FatalError: HailException: Expected identifier but found integer '0'. | |
| <input>:1:(ToArray (StreamMap __uid_3356 (ToStream False (GetField rows (TableCollect (TableMapRows (MatrixColsTable (MatrixMapCols () (MatrixMapGlobals (MatrixMapCols None (MatrixMapRows (MatrixMapRows (MatrixMapRows (MatrixMapRows (MatrixMapEntries (MatrixMapRows (MatrixUnionRows (MatrixKeyRowsBy (locus alleles) True (MatrixMapRows (MatrixKeyRowsBy (locus) False (MatrixExplodeRows (__uid_3321) (MatrixMapRows (MatrixMapRows (MatrixAnnotateRowsTable "__uid_3319" False (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa))))) (TableAggregateByKey (TableMapRows (TableKeyBy (locus alleles) False (TableLeftJoinRightDistinct __uid_3316 (TableKeyBy (__uid_3317) False (TableMapRows (TableKeyBy () False (TableExplode ("geneIds") (TableMapRows (MatrixRowsTable (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa)))))) (InsertFields (SelectFields (locus alleles geneIds) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref row))) None)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (__uid_3317 (GetField geneIds (Ref row)))))) (TableKeyBy (geneIds) False (JavaTable m9)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (GenCC (GetField __uid_3316 (Ref row))))) (MakeStruct (__uid_3318 (ApplyAggOp Collect () ((SelectFields (geneIds GenCC) (SelectFields (locus alleles geneIds GenCC) (Ref row))))))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref va)) None (GenCC (ToArray (StreamMap __uid_3320 (ToStream False (GetField __uid_3318 (GetField __uid_3319 (Ref va)))) (GetField GenCC (Ref __uid_3320))))))) (Let __cse_1 (GetField alleles (Ref va)) (Let __cse_2 (GetField locus (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC) (Ref va)) None (__uid_3321 (ArraySort __uid_3327 __uid_3328 (ToStream False (ToArray (StreamFlatMap __uid_3325 (ToStream False (ToArray (StreamFilter __uid_3322 (ToStream False (ToArray (StreamRange 15192 False (I32 1) (ArrayLen (CastToArray (Ref __cse_1))) (I32 1)))) (ApplyComparisonOp `!=` (Apply 15193 indexArray () String (Ref __cse_1) (Ref __uid_3322)) (Str "*"))))) (ToStream False (Let __uid_3326 (Apply 15199 min_rep () Struct{locus:Locus(GRCh38),alleles:Array[String]} (Ref __cse_2) (MakeArray Array[String] (Apply 15197 indexArray () String (Ref __cse_1) (I32 0)) (Apply 15198 indexArray () String (Ref __cse_1) (Ref __uid_3325)))) (If (ApplyComparisonOp `==` (GetField locus (Ref __uid_3326)) (Ref __cse_2)) (MakeArray Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}] (MakeStruct (alleles (GetField alleles (Ref __uid_3326))) (locus (GetField locus (Ref __uid_3326))) (a_index (Ref __uid_3325)) (was_split (ApplyComparisonOp `>` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2))))) (NA Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}]))))))) (If (IsNA (Ref __uid_3327)) (False) (If (IsNA (Ref __uid_3328)) (True) (If (False) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3328) (Ref __uid_3327)) (I32 0)) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3327) (Ref __uid_3328)) (I32 0))))))))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Let __uid_3329 (GetField __uid_3321 (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC __uid_3321) (Ref va)) None (locus (GetField locus (Ref __uid_3329))) (alleles (GetField alleles (Ref __uid_3329))) (a_index (GetField a_index (Ref __uid_3329))) (was_split (GetField was_split (Ref __uid_3329))) (old_locus (GetField locus (Ref va))) (old_alleles (GetField alleles (Ref va)))))))) (MatrixKeyRowsBy (locus alleles) False (MatrixMapRows (MatrixKeyRowsBy () False (MatrixExplodeRows (__uid_3321) (MatrixMapRows (MatrixMapRows (MatrixAnnotateRowsTable "__uid_3319" False (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa))))) (TableAggregateByKey (TableMapRows (TableKeyBy (locus alleles) False (TableLeftJoinRightDistinct __uid_3316 (TableKeyBy (__uid_3317) False (TableMapRows (TableKeyBy () False (TableExplode ("geneIds") (TableMapRows (MatrixRowsTable (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa)))))) (InsertFields (SelectFields (locus alleles geneIds) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref row))) None)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (__uid_3317 (GetField geneIds (Ref row)))))) (TableKeyBy (geneIds) False (JavaTable m9)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (GenCC (GetField __uid_3316 (Ref row))))) (MakeStruct (__uid_3318 (ApplyAggOp Collect () ((SelectFields (geneIds GenCC) (SelectFields (locus alleles geneIds GenCC) (Ref row))))))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref va)) None (GenCC (ToArray (StreamMap __uid_3320 (ToStream False (GetField __uid_3318 (GetField __uid_3319 (Ref va)))) (GetField GenCC (Ref __uid_3320))))))) (Let __cse_3 (GetField alleles (Ref va)) (Let __cse_4 (GetField locus (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC) (Ref va)) None (__uid_3321 (ArraySort __uid_3334 __uid_3335 (ToStream False (ToArray (StreamFlatMap __uid_3332 (ToStream False (ToArray (StreamFilter __uid_3322 (ToStream False (ToArray (StreamRange 15192 False (I32 1) (ArrayLen (CastToArray (Ref __cse_3))) (I32 1)))) (ApplyComparisonOp `!=` (Apply 15193 indexArray () String (Ref __cse_3) (Ref __uid_3322)) (Str "*"))))) (ToStream False (Let __uid_3333 (Apply 15205 min_rep () Struct{locus:Locus(GRCh38),alleles:Array[String]} (Ref __cse_4) (MakeArray Array[String] (Apply 15203 indexArray () String (Ref __cse_3) (I32 0)) (Apply 15204 indexArray () String (Ref __cse_3) (Ref __uid_3332)))) (If (ApplyComparisonOp `!=` (GetField locus (Ref __uid_3333)) (Ref __cse_4)) (MakeArray Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}] (MakeStruct (alleles (GetField alleles (Ref __uid_3333))) (locus (GetField locus (Ref __uid_3333))) (a_index (Ref __uid_3332)) (was_split (ApplyComparisonOp `>` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2))))) (NA Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}]))))))) (If (IsNA (Ref __uid_3334)) (False) (If (IsNA (Ref __uid_3335)) (True) (If (False) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3335) (Ref __uid_3334)) (I32 0)) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3334) (Ref __uid_3335)) (I32 0))))))))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Let __uid_3336 (GetField __uid_3321 (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC __uid_3321) (Ref va)) None (locus (GetField locus (Ref __uid_3336))) (alleles (GetField alleles (Ref __uid_3336))) (a_index (GetField a_index (Ref __uid_3336))) (was_split (GetField was_split (Ref __uid_3336))) (old_locus (GetField locus (Ref va))) (old_alleles (GetField alleles (Ref va))))))))) (Let __cse_5 (GetField vep (Ref va)) (Let __cse_6 (GetField a_index (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Ref va)) None (vep (InsertFields (Ref __cse_5) None (intergenic_consequences (ToArray (StreamFilter __uid_3337 (ToStream False (GetField intergenic_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3337)) (Ref __cse_6))))) (motif_feature_consequences (ToArray (StreamFilter __uid_3338 (ToStream False (GetField motif_feature_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3338)) (Ref __cse_6))))) (regulatory_feature_consequences (ToArray (StreamFilter __uid_3339 (ToStream False (GetField regulatory_feature_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3339)) (Ref __cse_6))))) (transcript_consequences (ToArray (StreamFilter __uid_3340 (ToStream False (GetField transcript_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3340)) (Ref __cse_6))))))))))) (Let __cse_10 (GetField a_index (Ref va)) (Let __cse_9 (If (ApplyUnaryPrimOp `!` (IsNA (GetField PL (Ref g)))) (ToArray (StreamMap __uid_3342 (ToStream False (ToArray (StreamRange 15210 False (I32 0) (I32 3) (I32 1)))) (Apply 15217 min () Int32 (ToArray (StreamFilter __uid_3345 (ToStream False (ToArray (StreamMap __uid_3344 (ToStream False (ToArray (StreamFilter __uid_3343 (ToStream False (ToArray (StreamRange 15212 False (I32 0) (Apply 15211 triangle () Int32 (ArrayLen (CastToArray (GetField old_alleles (Ref va))))) (I32 1)))) (ApplyComparisonOp `==` (Apply 15215 unphasedDiploidGtIndex () Int32 (Apply 15214 downcode () Call (Apply 15213 UnphasedDiploidGtIndexCall () Call (Ref __uid_3343)) (GetField a_index (Ref va)))) (Ref __uid_3342))))) (Apply 15216 indexArray () Int32 (GetField PL (Ref g)) (Ref __uid_3344))))) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3345)))))))) (NA Array[Int32])) (InsertFields (SelectFields (AD DP GQ GT MIN_DP PGT PID PL PS RGQ SB) (Ref g)) None (GT (Apply 15206 downcode () Call (GetField GT (Ref g)) (Ref __cse_10))) (DP (GetField DP (Ref g))) (AD (If (ApplyUnaryPrimOp `!` (IsNA (GetField AD (Ref g)))) (Let __cse_7 (GetField AD (Ref g)) (Let __cse_8 (GetField a_index (Ref va)) (MakeArray Array[Int32] (ApplyBinaryPrimOp `-` (Apply 15207 sum () Int32 (ToArray (StreamFilter __uid_3341 (ToStream False (Ref __cse_7)) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3341)))))) (Apply 15208 indexArray () Int32 (Ref __cse_7) (Ref __cse_8))) (Apply 15209 indexArray () Int32 (Ref __cse_7) (Ref __cse_8))))) (NA Array[Int32]))) (PL (Ref __cse_9)) (GQ (Coalesce (Apply 15218 gqFromPL () Int32 (Ref __cse_9)) (GetField GQ (Ref g)))) (PGT (Apply 15219 downcode () Call (GetField PGT (Ref g)) (Ref __cse_10))) (PID (GetField PID (Ref g))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (aIndex (GetField aIndex (Ref va))) (AC (GetField AC (Ref va))) (AF (GetField AF (Ref va))) (alt (GetField alt (Ref va))) (AN (GetField AN (Ref va))) (cadd (GetField cadd (Ref va))) (clinvar (GetField clinvar (Ref va))) (codingGeneIds (GetField codingGeneIds (Ref va))) (contig (GetField contig (Ref va))) (dbnsfp (GetField dbnsfp (Ref va))) (docId (GetField docId (Ref va))) (domains (GetField domains (Ref va))) (eigen (GetField eigen (Ref va))) (end (GetField end (Ref va))) (exac (GetField exac (Ref va))) (filters (GetField filters (Ref va))) (g1k (GetField g1k (Ref va))) (geneIds (GetField geneIds (Ref va))) (geno2mp (GetField geno2mp (Ref va))) (genotypes (GetField genotypes (Ref va))) (gnomad_exome_coverage (GetField gnomad_exome_coverage (Ref va))) (gnomad_exomes (GetField gnomad_exomes (Ref va))) (gnomad_genome_coverage (GetField gnomad_genome_coverage (Ref va))) (gnomad_genomes (GetField gnomad_genomes (Ref va))) (mainTranscript (GetField mainTranscript (Ref va))) (mpc (GetField mpc (Ref va))) (originalAltAlleles (GetField originalAltAlleles (Ref va))) (pos (GetField pos (Ref va))) (primate_ai (GetField primate_ai (Ref va))) (ref (GetField ref (Ref va))) (rg37_locus (GetField rg37_locus (Ref va))) (rsid (GetField rsid (Ref va))) (samples_ab (GetField samples_ab (Ref va))) (samples_gq (GetField samples_gq (Ref va))) (samples_no_call (GetField samples_no_call (Ref va))) (samples_num_alt (GetField samples_num_alt (Ref va))) (sortedTranscriptConsequences (GetField sortedTranscriptConsequences (Ref va))) (splice_ai (GetField splice_ai (Ref va))) (start (GetField start (Ref va))) (topmed (GetField topmed (Ref va))) (transcriptConsequenceTerms (GetField transcriptConsequenceTerms (Ref va))) (transcriptIds (GetField transcriptIds (Ref va))) (variantId (GetField variantId (Ref va))) (vep (GetField vep (Ref va))) (wasSplit (GetField wasSplit (Ref va))) (xpos (GetField xpos (Ref va))) (xstart (GetField xstart (Ref va))) (xstop (GetField xstop (Ref va))) (GenCC (GetField GenCC (Ref va))) (a_index (GetField a_index (Ref va))) (was_split (GetField was_split (Ref va))) (old_locus (GetField old_locus (Ref va))) (old_alleles (GetField old_alleles (Ref va)))))) (AggLet __cse_11 False (GetField GT (Ref g)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split) (Ref va)) None (variant_qc (Let __uid_3352 (MakeStruct (n_called (ApplyAggOp Sum () ((Apply 15234 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __cse_11))))))) (n_not_called (ApplyAggOp Sum () ((Apply 15235 toInt64 () Int64 (IsNA (Ref __cse_11)))))) (n_filtered (ApplyBinaryPrimOp `-` (Apply 15236 toInt64 () Int64 (Ref n_cols)) (ApplyAggOp Count () ()))) (call_stats (ApplyAggOp CallStats ((ArrayLen (CastToArray (GetField alleles (Ref va))))) ((Ref __cse_11))))) (Let __cse_18 (GetField call_stats (Ref __uid_3352)) (Let __cse_22 (GetField homozygote_count (Ref __cse_18)) (Let __cse_19 (GetField n_called (Ref __uid_3352)) (Let __cse_20 (GetField n_not_called (Ref __uid_3352)) (Let __cse_21 (GetField n_filtered (Ref __uid_3352)) (Let __uid_3353 (If (ApplyComparisonOp `==` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2)) (Let __cse_12 (GetField call_stats (Ref __uid_3352)) (Let __cse_13 (GetField homozygote_count (Ref __cse_12)) (Apply 15241 hardy_weinberg_test () Struct{het_freq_hwe:Float64,p_value:Float64} (Apply 15237 indexArray () Int32 (Ref __cse_13) (I32 0)) (ApplyBinaryPrimOp `-` (Apply 15238 indexArray () Int32 (GetField AC (Ref __cse_12)) (I32 1)) (ApplyBinaryPrimOp `*` (I32 2) (Apply 15239 indexArray () Int32 (Ref __cse_13) (I32 1)))) (Apply 15240 indexArray () Int32 (Ref __cse_13) (I32 1))))) (NA Struct{het_freq_hwe:Float64,p_value:Float64})) (MakeStruct (dp_stats (SelectFields (mean stdev min max) (AggLet __uid_agg3346 False (Apply 15220 toFloat64 () Float64 (GetField DP (Ref g))) (Let __uid_3347 (MakeStruct (n_def (ApplyAggOp Sum () ((Apply 15221 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_agg3346))))))) (sum (ApplyAggOp Sum () ((Ref __uid_agg3346)))) (sumsq (ApplyAggOp Sum () ((Apply 15223 pow () Float64 (Ref __uid_agg3346) (Apply 15222 toFloat64 () Float64 (I32 2)))))) (min (ApplyAggOp Min () ((Ref __uid_agg3346)))) (max (ApplyAggOp Max () ((Ref __uid_agg3346))))) (Let __cse_14 (GetField sum (Ref __uid_3347)) (Let __cse_15 (GetField n_def (Ref __uid_3347)) (Let __uid_3348 (ApplyBinaryPrimOp `/` (Ref __cse_14) (Apply 15224 toFloat64 () Float64 (Ref __cse_15))) (MakeStruct (mean (Ref __uid_3348)) (stdev (Apply 15226 sqrt () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (GetField sumsq (Ref __uid_3347)) (ApplyBinaryPrimOp `*` (Ref __uid_3348) (Ref __cse_14))) (Apply 15225 toFloat64 () Float64 (Ref __cse_15))))) (min (GetField min (Ref __uid_3347))) (max (GetField max (Ref __uid_3347))) (n (Ref __cse_15)) (sum (Ref __cse_14)))))))))) (gq_stats (SelectFields (mean stdev min max) (AggLet __uid_agg3349 False (Apply 15227 toFloat64 () Float64 (GetField GQ (Ref g))) (Let __uid_3350 (MakeStruct (n_def (ApplyAggOp Sum () ((Apply 15228 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_agg3349))))))) (sum (ApplyAggOp Sum () ((Ref __uid_agg3349)))) (sumsq (ApplyAggOp Sum () ((Apply 15230 pow () Float64 (Ref __uid_agg3349) (Apply 15229 toFloat64 () Float64 (I32 2)))))) (min (ApplyAggOp Min () ((Ref __uid_agg3349)))) (max (ApplyAggOp Max () ((Ref __uid_agg3349))))) (Let __cse_16 (GetField sum (Ref __uid_3350)) (Let __cse_17 (GetField n_def (Ref __uid_3350)) (Let __uid_3351 (ApplyBinaryPrimOp `/` (Ref __cse_16) (Apply 15231 toFloat64 () Float64 (Ref __cse_17))) (MakeStruct (mean (Ref __uid_3351)) (stdev (Apply 15233 sqrt () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (GetField sumsq (Ref __uid_3350)) (ApplyBinaryPrimOp `*` (Ref __uid_3351) (Ref __cse_16))) (Apply 15232 toFloat64 () Float64 (Ref __cse_17))))) (min (GetField min (Ref __uid_3350))) (max (GetField max (Ref __uid_3350))) (n (Ref __cse_17)) (sum (Ref __cse_16)))))))))) (AC (GetField AC (Ref __cse_18))) (AF (GetField AF (Ref __cse_18))) (AN (GetField AN (Ref __cse_18))) (homozygote_count (Ref __cse_22)) (call_rate (ApplyBinaryPrimOp `/` (Apply 15242 toFloat64 () Float64 (Ref __cse_19)) (Apply 15243 toFloat64 () Float64 (ApplyBinaryPrimOp `+` (ApplyBinaryPrimOp `+` (Ref __cse_19) (Ref __cse_20)) (Ref __cse_21))))) (n_called (Ref __cse_19)) (n_not_called (Ref __cse_20)) (n_filtered (Ref __cse_21)) (n_het (ApplyBinaryPrimOp `-` (Ref __cse_19) (Apply 15245 toInt64 () Int64 (Apply 15244 sum () Int32 (ToArray (StreamFilter __uid_3354 (ToStream False (Ref __cse_22)) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3354))))))))) (n_non_ref (ApplyBinaryPrimOp `-` (Ref __cse_19) (Apply 15247 toInt64 () Int64 (Apply 15246 indexArray () Int32 (Ref __cse_22) (I32 0))))) (het_freq_hwe (GetField het_freq_hwe (Ref __uid_3353))) (p_value_hwe (GetField p_value (Ref __uid_3353))))))))))))))) (Let __cse_23 (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)) (Let __cse_26 (If (Apply 15251 land () Boolean (ApplyComparisonOp `>=` (Ref __cse_23) (Apply 15249 toFloat64 () Float64 (I32 0))) (ApplyComparisonOp `<=` (Ref __cse_23) (Apply 15250 toFloat64 () Float64 (I32 1)))) (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)) (Die Float64 15254 (Apply 15253 concat () String (Str "de_novo: expect 0 <= pop_frequency_prior <= 1, found ") (Apply 15252 str () String (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)))))) (AggLet __cse_25 False (GetField GT (Ref g)) (Let __cse_24 (ApplyAggOp Sum () ((Apply 15256 toInt64 () Int64 (Apply 15255 nNonRefAlleles () Int32 (Ref __cse_25))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split variant_qc) (Ref va)) None (__prior (Ref __cse_26)) (__alt_alleles (Ref __cse_24)) (__site_freq (Apply 15261 max_ignore_missing () Float64 (Apply 15260 max_ignore_missing () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (Ref __cse_24) (Apply 15259 toInt64 () Int64 (I32 1))) (ApplyBinaryPrimOp `*` (Apply 15258 toInt64 () Int64 (I32 2)) (ApplyAggOp Sum () ((Apply 15257 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __cse_25)))))))) (Ref __cse_26)) (F64 3.3333333333333333e-06))))))))) (If (ApplyComparisonOp `==` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2)) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split variant_qc __prior __alt_alleles __site_freq) (Ref va)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],aIndex:Int32,AC:Int32,AF:Float64,alt:String,AN:Int32,cadd:Struct{PHRED:Float32},clinvar:Struct{allele_id:Int32,clinical_significance:String,gold_stars:Int32},codingGeneIds:Set[String],contig:String,dbnsfp:Struct{SIFT_pred:String,Polyphen2_HVAR_pred:String,MutationTaster_pred:String,FATHMM_pred:String,MetaSVM_pred:String,REVEL_score:String,GERP_RS:String,phastCons100way_vertebrate:String},docId:String,domains:Set[String],eigen:Struct{Eigen_phred:Float64},end:Int32,exac:Struct{AF_POPMAX:Float64,AF:Float64,AC_Adj:Int32,AC_Het:Int32,AC_Hom:Int32,AC_Hemi:Int32,AN_Adj:Int32},filters:Set[String],g1k:Struct{AC:Int32,AF:Float64,AN:Int32,POPMAX_AF:Float64},geneIds:Set[String],geno2mp:Struct{HPO_Count:Int32},genotypes:Array[Struct{num_alt:Int32,gq:Int32,ab:Float64,dp:Float64,sample_id:String}],gnomad_exome_coverage:Float64,gnomad_exomes:Struct{AF:Float64,AN:Int32,AC:Int32,FAF_AF:Float64,AF_POPMAX_OR_GLOBAL:Float64,Hom:Int32,Hemi:Int32},gnomad_genome_coverage:Float64,gnomad_genomes:Struct{AF:Float64,AN:Int32,AC:Int32,FAF_AF:Float64,AF_POPMAX_OR_GLOBAL:Float64,Hom:Int32,Hemi:Int32},mainTranscript:Struct{biotype:String,canonical:Int32,category:String,cdna_start:Int32,cdna_end:Int32,codons:String,gene_id:String,gene_symbol:String,hgvs:String,hgvsc:String,major_consequence:String,major_consequence_rank:Int32,transcript_id:String,amino_acids:String,domains:String,hgvsp:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,polyphen_prediction:String,protein_id:String,sift_prediction:String},mpc:Struct{MPC:String},originalAltAlleles:Array[String],pos:Int32,primate_ai:Struct{score:Float64},ref:String,rg37_locus:Locus(GRCh37),rsid:String,samples_ab:Struct{0_to_5:Set[String],5_to_10:Set[String],10_to_15:Set[String],15_to_20:Set[String],20_to_25:Set[String],25_to_30:Set[String],30_to_35:Set[String],35_to_40:Set[String],40_to_45:Set[String]},samples_gq:Struct{0_to_5:Set[String],5_to_10:Set[String],10_to_15:Set[String],15_to_20:Set[String],20_to_25:Set[String],25_to_30:Set[String],30_to_35:Set[String],35_to_40:Set[String],40_to_45:Set[String],45_to_50:Set[String],50_to_55:Set[String],55_to_60:Set[String],60_to_65:Set[String],65_to_70:Set[String],70_to_75:Set[String],75_to_80:Set[String],80_to_85:Set[String],85_to_90:Set[String],90_to_95:Set[String]},samples_no_call:Set[String],samples_num_alt:Struct{1:Set[String],2:Set[String]},sortedTranscriptConsequences:Array[Struct{biotype:String,canonical:Int32,cdna_start:Int32,cdna_end:Int32,codons:String,gene_id:String,gene_symbol:String,hgvsc:String,hgvsp:String,transcript_id:String,amino_acids:String,lof:String,lof_filter:String,lof_flags:String,lof_info:String,polyphen_prediction:String,protein_id:String,protein_start:Int32,sift_prediction:String,consequence_terms:Array[String],domains:Array[String],major_consequence:String,category:String,hgvs:String,major_consequence_rank:Int32,transcript_rank:Int32}],splice_ai:Struct{delta_score:Float32,splice_consequence:String},start:Int32,topmed:Struct{AC:Int32,AF:Float64,AN:Int32,Hom:Int32,Het:Int32},transcriptConsequenceTerms:Set[String],transcriptIds:Set[String],variantId:String,vep:Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,appris:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,tsl:Int32,uniparc:String,variant_allele:String}],variant_class:String},wasSplit:Boolean,xpos:Int64,xstart:Int64,xstop:Int64,GenCC:Array[Struct{gene_symbol:String,inheritance_class:String,LOEUF:Float64,missense:Float64}],a_index:Int32,was_split:Boolean,variant_qc:Struct{dp_stats:Struct{mean:Float64,stdev:Float64,min:Float64,max:Float64},gq_stats:Struct{mean:Float64,stdev:Float64,min:Float64,max:Float64},AC:Array[Int32],AF:Array[Float64],AN:Int32,homozygote_count:Array[Int32],call_rate:Float64,n_called:Int64,n_not_called:Int64,n_filtered:Int64,n_het:Int64,n_non_ref:Int64,het_freq_hwe:Float64,p_value_hwe:Float64},__prior:Float64,__alt_alleles:Int64,__site_freq:Float64} 15267 (Apply 15266 concat () String (Apply 15264 concat () String (Apply 15263 concat () String (Str "'de_novo' expects biallelic variants ('alleles' field of length 2), found ") (Apply 15262 str () String (GetField locus (Ref va)))) (Str ", ")) (Apply 15265 str () String (GetField alleles (Ref va))))))) (InsertFields (SelectFields (s) (SelectFields (s cmg_data) (Ref sa))) None)) (InsertFields (SelectFields () (SelectFields (gencodeVersion sourceFilePath genomeVersion sampleType hail_version) (Ref global))) None)) (SelectFields (s) (Ref sa)))) (InsertFields (SelectFields (s) (SelectFields (s) (Ref row))) None))))) (GetField s (Ref __uid_3356)))) | |
| ^ | |
| Java stack trace: | |
| is.hail.utils.HailException: Expected identifier but found integer '0'. | |
| <input>:1:(ToArray (StreamMap __uid_3356 (ToStream False (GetField rows (TableCollect (TableMapRows (MatrixColsTable (MatrixMapCols () (MatrixMapGlobals (MatrixMapCols None (MatrixMapRows (MatrixMapRows (MatrixMapRows (MatrixMapRows (MatrixMapEntries (MatrixMapRows (MatrixUnionRows (MatrixKeyRowsBy (locus alleles) True (MatrixMapRows (MatrixKeyRowsBy (locus) False (MatrixExplodeRows (__uid_3321) (MatrixMapRows (MatrixMapRows (MatrixAnnotateRowsTable "__uid_3319" False (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa))))) (TableAggregateByKey (TableMapRows (TableKeyBy (locus alleles) False (TableLeftJoinRightDistinct __uid_3316 (TableKeyBy (__uid_3317) False (TableMapRows (TableKeyBy () False (TableExplode ("geneIds") (TableMapRows (MatrixRowsTable (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa)))))) (InsertFields (SelectFields (locus alleles geneIds) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref row))) None)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (__uid_3317 (GetField geneIds (Ref row)))))) (TableKeyBy (geneIds) False (JavaTable m9)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (GenCC (GetField __uid_3316 (Ref row))))) (MakeStruct (__uid_3318 (ApplyAggOp Collect () ((SelectFields (geneIds GenCC) (SelectFields (locus alleles geneIds GenCC) (Ref row))))))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref va)) None (GenCC (ToArray (StreamMap __uid_3320 (ToStream False (GetField __uid_3318 (GetField __uid_3319 (Ref va)))) (GetField GenCC (Ref __uid_3320))))))) (Let __cse_1 (GetField alleles (Ref va)) (Let __cse_2 (GetField locus (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC) (Ref va)) None (__uid_3321 (ArraySort __uid_3327 __uid_3328 (ToStream False (ToArray (StreamFlatMap __uid_3325 (ToStream False (ToArray (StreamFilter __uid_3322 (ToStream False (ToArray (StreamRange 15192 False (I32 1) (ArrayLen (CastToArray (Ref __cse_1))) (I32 1)))) (ApplyComparisonOp `!=` (Apply 15193 indexArray () String (Ref __cse_1) (Ref __uid_3322)) (Str "*"))))) (ToStream False (Let __uid_3326 (Apply 15199 min_rep () Struct{locus:Locus(GRCh38),alleles:Array[String]} (Ref __cse_2) (MakeArray Array[String] (Apply 15197 indexArray () String (Ref __cse_1) (I32 0)) (Apply 15198 indexArray () String (Ref __cse_1) (Ref __uid_3325)))) (If (ApplyComparisonOp `==` (GetField locus (Ref __uid_3326)) (Ref __cse_2)) (MakeArray Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}] (MakeStruct (alleles (GetField alleles (Ref __uid_3326))) (locus (GetField locus (Ref __uid_3326))) (a_index (Ref __uid_3325)) (was_split (ApplyComparisonOp `>` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2))))) (NA Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}]))))))) (If (IsNA (Ref __uid_3327)) (False) (If (IsNA (Ref __uid_3328)) (True) (If (False) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3328) (Ref __uid_3327)) (I32 0)) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3327) (Ref __uid_3328)) (I32 0))))))))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Let __uid_3329 (GetField __uid_3321 (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC __uid_3321) (Ref va)) None (locus (GetField locus (Ref __uid_3329))) (alleles (GetField alleles (Ref __uid_3329))) (a_index (GetField a_index (Ref __uid_3329))) (was_split (GetField was_split (Ref __uid_3329))) (old_locus (GetField locus (Ref va))) (old_alleles (GetField alleles (Ref va)))))))) (MatrixKeyRowsBy (locus alleles) False (MatrixMapRows (MatrixKeyRowsBy () False (MatrixExplodeRows (__uid_3321) (MatrixMapRows (MatrixMapRows (MatrixAnnotateRowsTable "__uid_3319" False (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa))))) (TableAggregateByKey (TableMapRows (TableKeyBy (locus alleles) False (TableLeftJoinRightDistinct __uid_3316 (TableKeyBy (__uid_3317) False (TableMapRows (TableKeyBy () False (TableExplode ("geneIds") (TableMapRows (MatrixRowsTable (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa)))))) (InsertFields (SelectFields (locus alleles geneIds) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref row))) None)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (__uid_3317 (GetField geneIds (Ref row)))))) (TableKeyBy (geneIds) False (JavaTable m9)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (GenCC (GetField __uid_3316 (Ref row))))) (MakeStruct (__uid_3318 (ApplyAggOp Collect () ((SelectFields (geneIds GenCC) (SelectFields (locus alleles geneIds GenCC) (Ref row))))))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref va)) None (GenCC (ToArray (StreamMap __uid_3320 (ToStream False (GetField __uid_3318 (GetField __uid_3319 (Ref va)))) (GetField GenCC (Ref __uid_3320))))))) (Let __cse_3 (GetField alleles (Ref va)) (Let __cse_4 (GetField locus (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC) (Ref va)) None (__uid_3321 (ArraySort __uid_3334 __uid_3335 (ToStream False (ToArray (StreamFlatMap __uid_3332 (ToStream False (ToArray (StreamFilter __uid_3322 (ToStream False (ToArray (StreamRange 15192 False (I32 1) (ArrayLen (CastToArray (Ref __cse_3))) (I32 1)))) (ApplyComparisonOp `!=` (Apply 15193 indexArray () String (Ref __cse_3) (Ref __uid_3322)) (Str "*"))))) (ToStream False (Let __uid_3333 (Apply 15205 min_rep () Struct{locus:Locus(GRCh38),alleles:Array[String]} (Ref __cse_4) (MakeArray Array[String] (Apply 15203 indexArray () String (Ref __cse_3) (I32 0)) (Apply 15204 indexArray () String (Ref __cse_3) (Ref __uid_3332)))) (If (ApplyComparisonOp `!=` (GetField locus (Ref __uid_3333)) (Ref __cse_4)) (MakeArray Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}] (MakeStruct (alleles (GetField alleles (Ref __uid_3333))) (locus (GetField locus (Ref __uid_3333))) (a_index (Ref __uid_3332)) (was_split (ApplyComparisonOp `>` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2))))) (NA Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}]))))))) (If (IsNA (Ref __uid_3334)) (False) (If (IsNA (Ref __uid_3335)) (True) (If (False) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3335) (Ref __uid_3334)) (I32 0)) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3334) (Ref __uid_3335)) (I32 0))))))))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Let __uid_3336 (GetField __uid_3321 (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC __uid_3321) (Ref va)) None (locus (GetField locus (Ref __uid_3336))) (alleles (GetField alleles (Ref __uid_3336))) (a_index (GetField a_index (Ref __uid_3336))) (was_split (GetField was_split (Ref __uid_3336))) (old_locus (GetField locus (Ref va))) (old_alleles (GetField alleles (Ref va))))))))) (Let __cse_5 (GetField vep (Ref va)) (Let __cse_6 (GetField a_index (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Ref va)) None (vep (InsertFields (Ref __cse_5) None (intergenic_consequences (ToArray (StreamFilter __uid_3337 (ToStream False (GetField intergenic_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3337)) (Ref __cse_6))))) (motif_feature_consequences (ToArray (StreamFilter __uid_3338 (ToStream False (GetField motif_feature_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3338)) (Ref __cse_6))))) (regulatory_feature_consequences (ToArray (StreamFilter __uid_3339 (ToStream False (GetField regulatory_feature_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3339)) (Ref __cse_6))))) (transcript_consequences (ToArray (StreamFilter __uid_3340 (ToStream False (GetField transcript_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3340)) (Ref __cse_6))))))))))) (Let __cse_10 (GetField a_index (Ref va)) (Let __cse_9 (If (ApplyUnaryPrimOp `!` (IsNA (GetField PL (Ref g)))) (ToArray (StreamMap __uid_3342 (ToStream False (ToArray (StreamRange 15210 False (I32 0) (I32 3) (I32 1)))) (Apply 15217 min () Int32 (ToArray (StreamFilter __uid_3345 (ToStream False (ToArray (StreamMap __uid_3344 (ToStream False (ToArray (StreamFilter __uid_3343 (ToStream False (ToArray (StreamRange 15212 False (I32 0) (Apply 15211 triangle () Int32 (ArrayLen (CastToArray (GetField old_alleles (Ref va))))) (I32 1)))) (ApplyComparisonOp `==` (Apply 15215 unphasedDiploidGtIndex () Int32 (Apply 15214 downcode () Call (Apply 15213 UnphasedDiploidGtIndexCall () Call (Ref __uid_3343)) (GetField a_index (Ref va)))) (Ref __uid_3342))))) (Apply 15216 indexArray () Int32 (GetField PL (Ref g)) (Ref __uid_3344))))) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3345)))))))) (NA Array[Int32])) (InsertFields (SelectFields (AD DP GQ GT MIN_DP PGT PID PL PS RGQ SB) (Ref g)) None (GT (Apply 15206 downcode () Call (GetField GT (Ref g)) (Ref __cse_10))) (DP (GetField DP (Ref g))) (AD (If (ApplyUnaryPrimOp `!` (IsNA (GetField AD (Ref g)))) (Let __cse_7 (GetField AD (Ref g)) (Let __cse_8 (GetField a_index (Ref va)) (MakeArray Array[Int32] (ApplyBinaryPrimOp `-` (Apply 15207 sum () Int32 (ToArray (StreamFilter __uid_3341 (ToStream False (Ref __cse_7)) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3341)))))) (Apply 15208 indexArray () Int32 (Ref __cse_7) (Ref __cse_8))) (Apply 15209 indexArray () Int32 (Ref __cse_7) (Ref __cse_8))))) (NA Array[Int32]))) (PL (Ref __cse_9)) (GQ (Coalesce (Apply 15218 gqFromPL () Int32 (Ref __cse_9)) (GetField GQ (Ref g)))) (PGT (Apply 15219 downcode () Call (GetField PGT (Ref g)) (Ref __cse_10))) (PID (GetField PID (Ref g))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (aIndex (GetField aIndex (Ref va))) (AC (GetField AC (Ref va))) (AF (GetField AF (Ref va))) (alt (GetField alt (Ref va))) (AN (GetField AN (Ref va))) (cadd (GetField cadd (Ref va))) (clinvar (GetField clinvar (Ref va))) (codingGeneIds (GetField codingGeneIds (Ref va))) (contig (GetField contig (Ref va))) (dbnsfp (GetField dbnsfp (Ref va))) (docId (GetField docId (Ref va))) (domains (GetField domains (Ref va))) (eigen (GetField eigen (Ref va))) (end (GetField end (Ref va))) (exac (GetField exac (Ref va))) (filters (GetField filters (Ref va))) (g1k (GetField g1k (Ref va))) (geneIds (GetField geneIds (Ref va))) (geno2mp (GetField geno2mp (Ref va))) (genotypes (GetField genotypes (Ref va))) (gnomad_exome_coverage (GetField gnomad_exome_coverage (Ref va))) (gnomad_exomes (GetField gnomad_exomes (Ref va))) (gnomad_genome_coverage (GetField gnomad_genome_coverage (Ref va))) (gnomad_genomes (GetField gnomad_genomes (Ref va))) (mainTranscript (GetField mainTranscript (Ref va))) (mpc (GetField mpc (Ref va))) (originalAltAlleles (GetField originalAltAlleles (Ref va))) (pos (GetField pos (Ref va))) (primate_ai (GetField primate_ai (Ref va))) (ref (GetField ref (Ref va))) (rg37_locus (GetField rg37_locus (Ref va))) (rsid (GetField rsid (Ref va))) (samples_ab (GetField samples_ab (Ref va))) (samples_gq (GetField samples_gq (Ref va))) (samples_no_call (GetField samples_no_call (Ref va))) (samples_num_alt (GetField samples_num_alt (Ref va))) (sortedTranscriptConsequences (GetField sortedTranscriptConsequences (Ref va))) (splice_ai (GetField splice_ai (Ref va))) (start (GetField start (Ref va))) (topmed (GetField topmed (Ref va))) (transcriptConsequenceTerms (GetField transcriptConsequenceTerms (Ref va))) (transcriptIds (GetField transcriptIds (Ref va))) (variantId (GetField variantId (Ref va))) (vep (GetField vep (Ref va))) (wasSplit (GetField wasSplit (Ref va))) (xpos (GetField xpos (Ref va))) (xstart (GetField xstart (Ref va))) (xstop (GetField xstop (Ref va))) (GenCC (GetField GenCC (Ref va))) (a_index (GetField a_index (Ref va))) (was_split (GetField was_split (Ref va))) (old_locus (GetField old_locus (Ref va))) (old_alleles (GetField old_alleles (Ref va)))))) (AggLet __cse_11 False (GetField GT (Ref g)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split) (Ref va)) None (variant_qc (Let __uid_3352 (MakeStruct (n_called (ApplyAggOp Sum () ((Apply 15234 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __cse_11))))))) (n_not_called (ApplyAggOp Sum () ((Apply 15235 toInt64 () Int64 (IsNA (Ref __cse_11)))))) (n_filtered (ApplyBinaryPrimOp `-` (Apply 15236 toInt64 () Int64 (Ref n_cols)) (ApplyAggOp Count () ()))) (call_stats (ApplyAggOp CallStats ((ArrayLen (CastToArray (GetField alleles (Ref va))))) ((Ref __cse_11))))) (Let __cse_18 (GetField call_stats (Ref __uid_3352)) (Let __cse_22 (GetField homozygote_count (Ref __cse_18)) (Let __cse_19 (GetField n_called (Ref __uid_3352)) (Let __cse_20 (GetField n_not_called (Ref __uid_3352)) (Let __cse_21 (GetField n_filtered (Ref __uid_3352)) (Let __uid_3353 (If (ApplyComparisonOp `==` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2)) (Let __cse_12 (GetField call_stats (Ref __uid_3352)) (Let __cse_13 (GetField homozygote_count (Ref __cse_12)) (Apply 15241 hardy_weinberg_test () Struct{het_freq_hwe:Float64,p_value:Float64} (Apply 15237 indexArray () Int32 (Ref __cse_13) (I32 0)) (ApplyBinaryPrimOp `-` (Apply 15238 indexArray () Int32 (GetField AC (Ref __cse_12)) (I32 1)) (ApplyBinaryPrimOp `*` (I32 2) (Apply 15239 indexArray () Int32 (Ref __cse_13) (I32 1)))) (Apply 15240 indexArray () Int32 (Ref __cse_13) (I32 1))))) (NA Struct{het_freq_hwe:Float64,p_value:Float64})) (MakeStruct (dp_stats (SelectFields (mean stdev min max) (AggLet __uid_agg3346 False (Apply 15220 toFloat64 () Float64 (GetField DP (Ref g))) (Let __uid_3347 (MakeStruct (n_def (ApplyAggOp Sum () ((Apply 15221 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_agg3346))))))) (sum (ApplyAggOp Sum () ((Ref __uid_agg3346)))) (sumsq (ApplyAggOp Sum () ((Apply 15223 pow () Float64 (Ref __uid_agg3346) (Apply 15222 toFloat64 () Float64 (I32 2)))))) (min (ApplyAggOp Min () ((Ref __uid_agg3346)))) (max (ApplyAggOp Max () ((Ref __uid_agg3346))))) (Let __cse_14 (GetField sum (Ref __uid_3347)) (Let __cse_15 (GetField n_def (Ref __uid_3347)) (Let __uid_3348 (ApplyBinaryPrimOp `/` (Ref __cse_14) (Apply 15224 toFloat64 () Float64 (Ref __cse_15))) (MakeStruct (mean (Ref __uid_3348)) (stdev (Apply 15226 sqrt () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (GetField sumsq (Ref __uid_3347)) (ApplyBinaryPrimOp `*` (Ref __uid_3348) (Ref __cse_14))) (Apply 15225 toFloat64 () Float64 (Ref __cse_15))))) (min (GetField min (Ref __uid_3347))) (max (GetField max (Ref __uid_3347))) (n (Ref __cse_15)) (sum (Ref __cse_14)))))))))) (gq_stats (SelectFields (mean stdev min max) (AggLet __uid_agg3349 False (Apply 15227 toFloat64 () Float64 (GetField GQ (Ref g))) (Let __uid_3350 (MakeStruct (n_def (ApplyAggOp Sum () ((Apply 15228 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_agg3349))))))) (sum (ApplyAggOp Sum () ((Ref __uid_agg3349)))) (sumsq (ApplyAggOp Sum () ((Apply 15230 pow () Float64 (Ref __uid_agg3349) (Apply 15229 toFloat64 () Float64 (I32 2)))))) (min (ApplyAggOp Min () ((Ref __uid_agg3349)))) (max (ApplyAggOp Max () ((Ref __uid_agg3349))))) (Let __cse_16 (GetField sum (Ref __uid_3350)) (Let __cse_17 (GetField n_def (Ref __uid_3350)) (Let __uid_3351 (ApplyBinaryPrimOp `/` (Ref __cse_16) (Apply 15231 toFloat64 () Float64 (Ref __cse_17))) (MakeStruct (mean (Ref __uid_3351)) (stdev (Apply 15233 sqrt () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (GetField sumsq (Ref __uid_3350)) (ApplyBinaryPrimOp `*` (Ref __uid_3351) (Ref __cse_16))) (Apply 15232 toFloat64 () Float64 (Ref __cse_17))))) (min (GetField min (Ref __uid_3350))) (max (GetField max (Ref __uid_3350))) (n (Ref __cse_17)) (sum (Ref __cse_16)))))))))) (AC (GetField AC (Ref __cse_18))) (AF (GetField AF (Ref __cse_18))) (AN (GetField AN (Ref __cse_18))) (homozygote_count (Ref __cse_22)) (call_rate (ApplyBinaryPrimOp `/` (Apply 15242 toFloat64 () Float64 (Ref __cse_19)) (Apply 15243 toFloat64 () Float64 (ApplyBinaryPrimOp `+` (ApplyBinaryPrimOp `+` (Ref __cse_19) (Ref __cse_20)) (Ref __cse_21))))) (n_called (Ref __cse_19)) (n_not_called (Ref __cse_20)) (n_filtered (Ref __cse_21)) (n_het (ApplyBinaryPrimOp `-` (Ref __cse_19) (Apply 15245 toInt64 () Int64 (Apply 15244 sum () Int32 (ToArray (StreamFilter __uid_3354 (ToStream False (Ref __cse_22)) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3354))))))))) (n_non_ref (ApplyBinaryPrimOp `-` (Ref __cse_19) (Apply 15247 toInt64 () Int64 (Apply 15246 indexArray () Int32 (Ref __cse_22) (I32 0))))) (het_freq_hwe (GetField het_freq_hwe (Ref __uid_3353))) (p_value_hwe (GetField p_value (Ref __uid_3353))))))))))))))) (Let __cse_23 (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)) (Let __cse_26 (If (Apply 15251 land () Boolean (ApplyComparisonOp `>=` (Ref __cse_23) (Apply 15249 toFloat64 () Float64 (I32 0))) (ApplyComparisonOp `<=` (Ref __cse_23) (Apply 15250 toFloat64 () Float64 (I32 1)))) (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)) (Die Float64 15254 (Apply 15253 concat () String (Str "de_novo: expect 0 <= pop_frequency_prior <= 1, found ") (Apply 15252 str () String (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)))))) (AggLet __cse_25 False (GetField GT (Ref g)) (Let __cse_24 (ApplyAggOp Sum () ((Apply 15256 toInt64 () Int64 (Apply 15255 nNonRefAlleles () Int32 (Ref __cse_25))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split variant_qc) (Ref va)) None (__prior (Ref __cse_26)) (__alt_alleles (Ref __cse_24)) (__site_freq (Apply 15261 max_ignore_missing () Float64 (Apply 15260 max_ignore_missing () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (Ref __cse_24) (Apply 15259 toInt64 () Int64 (I32 1))) (ApplyBinaryPrimOp `*` (Apply 15258 toInt64 () Int64 (I32 2)) (ApplyAggOp Sum () ((Apply 15257 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __cse_25)))))))) (Ref __cse_26)) (F64 3.3333333333333333e-06))))))))) (If (ApplyComparisonOp `==` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2)) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split variant_qc __prior __alt_alleles __site_freq) (Ref va)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],aIndex:Int32,AC:Int32,AF:Float64,alt:String,AN:Int32,cadd:Struct{PHRED:Float32},clinvar:Struct{allele_id:Int32,clinical_significance:String,gold_stars:Int32},codingGeneIds:Set[String],contig:String,dbnsfp:Struct{SIFT_pred:String,Polyphen2_HVAR_pred:String,MutationTaster_pred:String,FATHMM_pred:String,MetaSVM_pred:String,REVEL_score:String,GERP_RS:String,phastCons100way_vertebrate:String},docId:String,domains:Set[String],eigen:Struct{Eigen_phred:Float64},end:Int32,exac:Struct{AF_POPMAX:Float64,AF:Float64,AC_Adj:Int32,AC_Het:Int32,AC_Hom:Int32,AC_Hemi:Int32,AN_Adj:Int32},filters:Set[String],g1k:Struct{AC:Int32,AF:Float64,AN:Int32,POPMAX_AF:Float64},geneIds:Set[String],geno2mp:Struct{HPO_Count:Int32},genotypes:Array[Struct{num_alt:Int32,gq:Int32,ab:Float64,dp:Float64,sample_id:String}],gnomad_exome_coverage:Float64,gnomad_exomes:Struct{AF:Float64,AN:Int32,AC:Int32,FAF_AF:Float64,AF_POPMAX_OR_GLOBAL:Float64,Hom:Int32,Hemi:Int32},gnomad_genome_coverage:Float64,gnomad_genomes:Struct{AF:Float64,AN:Int32,AC:Int32,FAF_AF:Float64,AF_POPMAX_OR_GLOBAL:Float64,Hom:Int32,Hemi:Int32},mainTranscript:Struct{biotype:String,canonical:Int32,category:String,cdna_start:Int32,cdna_end:Int32,codons:String,gene_id:String,gene_symbol:String,hgvs:String,hgvsc:String,major_consequence:String,major_consequence_rank:Int32,transcript_id:String,amino_acids:String,domains:String,hgvsp:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,polyphen_prediction:String,protein_id:String,sift_prediction:String},mpc:Struct{MPC:String},originalAltAlleles:Array[String],pos:Int32,primate_ai:Struct{score:Float64},ref:String,rg37_locus:Locus(GRCh37),rsid:String,samples_ab:Struct{0_to_5:Set[String],5_to_10:Set[String],10_to_15:Set[String],15_to_20:Set[String],20_to_25:Set[String],25_to_30:Set[String],30_to_35:Set[String],35_to_40:Set[String],40_to_45:Set[String]},samples_gq:Struct{0_to_5:Set[String],5_to_10:Set[String],10_to_15:Set[String],15_to_20:Set[String],20_to_25:Set[String],25_to_30:Set[String],30_to_35:Set[String],35_to_40:Set[String],40_to_45:Set[String],45_to_50:Set[String],50_to_55:Set[String],55_to_60:Set[String],60_to_65:Set[String],65_to_70:Set[String],70_to_75:Set[String],75_to_80:Set[String],80_to_85:Set[String],85_to_90:Set[String],90_to_95:Set[String]},samples_no_call:Set[String],samples_num_alt:Struct{1:Set[String],2:Set[String]},sortedTranscriptConsequences:Array[Struct{biotype:String,canonical:Int32,cdna_start:Int32,cdna_end:Int32,codons:String,gene_id:String,gene_symbol:String,hgvsc:String,hgvsp:String,transcript_id:String,amino_acids:String,lof:String,lof_filter:String,lof_flags:String,lof_info:String,polyphen_prediction:String,protein_id:String,protein_start:Int32,sift_prediction:String,consequence_terms:Array[String],domains:Array[String],major_consequence:String,category:String,hgvs:String,major_consequence_rank:Int32,transcript_rank:Int32}],splice_ai:Struct{delta_score:Float32,splice_consequence:String},start:Int32,topmed:Struct{AC:Int32,AF:Float64,AN:Int32,Hom:Int32,Het:Int32},transcriptConsequenceTerms:Set[String],transcriptIds:Set[String],variantId:String,vep:Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,appris:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,tsl:Int32,uniparc:String,variant_allele:String}],variant_class:String},wasSplit:Boolean,xpos:Int64,xstart:Int64,xstop:Int64,GenCC:Array[Struct{gene_symbol:String,inheritance_class:String,LOEUF:Float64,missense:Float64}],a_index:Int32,was_split:Boolean,variant_qc:Struct{dp_stats:Struct{mean:Float64,stdev:Float64,min:Float64,max:Float64},gq_stats:Struct{mean:Float64,stdev:Float64,min:Float64,max:Float64},AC:Array[Int32],AF:Array[Float64],AN:Int32,homozygote_count:Array[Int32],call_rate:Float64,n_called:Int64,n_not_called:Int64,n_filtered:Int64,n_het:Int64,n_non_ref:Int64,het_freq_hwe:Float64,p_value_hwe:Float64},__prior:Float64,__alt_alleles:Int64,__site_freq:Float64} 15267 (Apply 15266 concat () String (Apply 15264 concat () String (Apply 15263 concat () String (Str "'de_novo' expects biallelic variants ('alleles' field of length 2), found ") (Apply 15262 str () String (GetField locus (Ref va)))) (Str ", ")) (Apply 15265 str () String (GetField alleles (Ref va))))))) (InsertFields (SelectFields (s) (SelectFields (s cmg_data) (Ref sa))) None)) (InsertFields (SelectFields () (SelectFields (gencodeVersion sourceFilePath genomeVersion sampleType hail_version) (Ref global))) None)) (SelectFields (s) (Ref sa)))) (InsertFields (SelectFields (s) (SelectFields (s) (Ref row))) None))))) (GetField s (Ref __uid_3356)))) | |
| ^ | |
| at is.hail.utils.ErrorHandling.fatal(ErrorHandling.scala:11) | |
| at is.hail.utils.ErrorHandling.fatal$(ErrorHandling.scala:11) | |
| at is.hail.utils.package$.fatal(package.scala:77) | |
| at is.hail.expr.ParserUtils$.error(Parser.scala:34) | |
| at is.hail.expr.ir.IRParser$.error(Parser.scala:162) | |
| at is.hail.expr.ir.IRParser$.identifier(Parser.scala:190) | |
| at is.hail.expr.ir.IRParser$.struct_field(Parser.scala:359) | |
| at is.hail.expr.ir.IRParser$.type_field(Parser.scala:373) | |
| at is.hail.expr.ir.IRParser$.$anonfun$type_expr$4(Parser.scala:534) | |
| at is.hail.expr.ir.IRParser$.repsepUntil(Parser.scala:292) | |
| at is.hail.expr.ir.IRParser$.type_expr(Parser.scala:534) | |
| at is.hail.expr.ir.IRParser$.$anonfun$type_field$1(Parser.scala:373) | |
| at is.hail.expr.ir.IRParser$.struct_field(Parser.scala:361) | |
| at is.hail.expr.ir.IRParser$.type_field(Parser.scala:373) | |
| at is.hail.expr.ir.IRParser$.$anonfun$type_expr$4(Parser.scala:534) | |
| at is.hail.expr.ir.IRParser$.repsepUntil(Parser.scala:292) | |
| at is.hail.expr.ir.IRParser$.type_expr(Parser.scala:534) | |
| at is.hail.expr.ir.IRParser$.ir_value_expr_1(Parser.scala:1266) | |
| at is.hail.expr.ir.IRParser$.$anonfun$ir_value_expr$1(Parser.scala:782) | |
| at is.hail.utils.StackSafe$More.advance(StackSafe.scala:64) | |
| at is.hail.utils.StackSafe$.run(StackSafe.scala:16) | |
| at is.hail.utils.StackSafe$StackFrame.run(StackSafe.scala:32) | |
| at is.hail.expr.ir.IRParser$.$anonfun$parse_value_ir$1(Parser.scala:1970) | |
| at is.hail.expr.ir.IRParser$.parse(Parser.scala:1967) | |
| at is.hail.expr.ir.IRParser$.parse_value_ir(Parser.scala:1970) | |
| at is.hail.backend.spark.SparkBackend.$anonfun$parse_value_ir$2(SparkBackend.scala:637) | |
| at is.hail.expr.ir.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:47) | |
| at is.hail.utils.package$.using(package.scala:627) | |
| at is.hail.expr.ir.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:47) | |
| at is.hail.utils.package$.using(package.scala:627) | |
| at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17) | |
| at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:46) | |
| at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:275) | |
| at is.hail.backend.spark.SparkBackend.$anonfun$parse_value_ir$1(SparkBackend.scala:636) | |
| at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52) | |
| at is.hail.utils.ExecutionTimer$.logTime(ExecutionTimer.scala:59) | |
| at is.hail.backend.spark.SparkBackend.parse_value_ir(SparkBackend.scala:635) | |
| at jdk.internal.reflect.GeneratedMethodAccessor122.invoke(Unknown Source) | |
| at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) | |
| at java.base/java.lang.reflect.Method.invoke(Method.java:566) | |
| at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) | |
| at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) | |
| at py4j.Gateway.invoke(Gateway.java:282) | |
| at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) | |
| at py4j.commands.CallCommand.execute(CallCommand.java:79) | |
| at py4j.GatewayConnection.run(GatewayConnection.java:238) | |
| at java.base/java.lang.Thread.run(Thread.java:829) | |
| Hail version: 0.2.72-cfce5e858cab | |
| Error summary: HailException: Expected identifier but found integer '0'. | |
| <input>:1:(ToArray (StreamMap __uid_3356 (ToStream False (GetField rows (TableCollect (TableMapRows (MatrixColsTable (MatrixMapCols () (MatrixMapGlobals (MatrixMapCols None (MatrixMapRows (MatrixMapRows (MatrixMapRows (MatrixMapRows (MatrixMapEntries (MatrixMapRows (MatrixUnionRows (MatrixKeyRowsBy (locus alleles) True (MatrixMapRows (MatrixKeyRowsBy (locus) False (MatrixExplodeRows (__uid_3321) (MatrixMapRows (MatrixMapRows (MatrixAnnotateRowsTable "__uid_3319" False (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa))))) (TableAggregateByKey (TableMapRows (TableKeyBy (locus alleles) False (TableLeftJoinRightDistinct __uid_3316 (TableKeyBy (__uid_3317) False (TableMapRows (TableKeyBy () False (TableExplode ("geneIds") (TableMapRows (MatrixRowsTable (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa)))))) (InsertFields (SelectFields (locus alleles geneIds) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref row))) None)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (__uid_3317 (GetField geneIds (Ref row)))))) (TableKeyBy (geneIds) False (JavaTable m9)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (GenCC (GetField __uid_3316 (Ref row))))) (MakeStruct (__uid_3318 (ApplyAggOp Collect () ((SelectFields (geneIds GenCC) (SelectFields (locus alleles geneIds GenCC) (Ref row))))))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref va)) None (GenCC (ToArray (StreamMap __uid_3320 (ToStream False (GetField __uid_3318 (GetField __uid_3319 (Ref va)))) (GetField GenCC (Ref __uid_3320))))))) (Let __cse_1 (GetField alleles (Ref va)) (Let __cse_2 (GetField locus (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC) (Ref va)) None (__uid_3321 (ArraySort __uid_3327 __uid_3328 (ToStream False (ToArray (StreamFlatMap __uid_3325 (ToStream False (ToArray (StreamFilter __uid_3322 (ToStream False (ToArray (StreamRange 15192 False (I32 1) (ArrayLen (CastToArray (Ref __cse_1))) (I32 1)))) (ApplyComparisonOp `!=` (Apply 15193 indexArray () String (Ref __cse_1) (Ref __uid_3322)) (Str "*"))))) (ToStream False (Let __uid_3326 (Apply 15199 min_rep () Struct{locus:Locus(GRCh38),alleles:Array[String]} (Ref __cse_2) (MakeArray Array[String] (Apply 15197 indexArray () String (Ref __cse_1) (I32 0)) (Apply 15198 indexArray () String (Ref __cse_1) (Ref __uid_3325)))) (If (ApplyComparisonOp `==` (GetField locus (Ref __uid_3326)) (Ref __cse_2)) (MakeArray Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}] (MakeStruct (alleles (GetField alleles (Ref __uid_3326))) (locus (GetField locus (Ref __uid_3326))) (a_index (Ref __uid_3325)) (was_split (ApplyComparisonOp `>` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2))))) (NA Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}]))))))) (If (IsNA (Ref __uid_3327)) (False) (If (IsNA (Ref __uid_3328)) (True) (If (False) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3328) (Ref __uid_3327)) (I32 0)) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3327) (Ref __uid_3328)) (I32 0))))))))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Let __uid_3329 (GetField __uid_3321 (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC __uid_3321) (Ref va)) None (locus (GetField locus (Ref __uid_3329))) (alleles (GetField alleles (Ref __uid_3329))) (a_index (GetField a_index (Ref __uid_3329))) (was_split (GetField was_split (Ref __uid_3329))) (old_locus (GetField locus (Ref va))) (old_alleles (GetField alleles (Ref va)))))))) (MatrixKeyRowsBy (locus alleles) False (MatrixMapRows (MatrixKeyRowsBy () False (MatrixExplodeRows (__uid_3321) (MatrixMapRows (MatrixMapRows (MatrixAnnotateRowsTable "__uid_3319" False (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa))))) (TableAggregateByKey (TableMapRows (TableKeyBy (locus alleles) False (TableLeftJoinRightDistinct __uid_3316 (TableKeyBy (__uid_3317) False (TableMapRows (TableKeyBy () False (TableExplode ("geneIds") (TableMapRows (MatrixRowsTable (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3315" (MatrixFilterRows (JavaMatrix m7) (Coalesce (ApplyComparisonOp `<=` (GetField AF (GetField gnomad_exomes (Ref va))) (F64 0.01)) (False))) (TableKeyBy (s) False (JavaTable m8))) (InsertFields (SelectFields (s) (Ref sa)) None (cmg_data (GetField __uid_3315 (Ref sa)))))) (InsertFields (SelectFields (locus alleles geneIds) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref row))) None)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (__uid_3317 (GetField geneIds (Ref row)))))) (TableKeyBy (geneIds) False (JavaTable m9)))) (InsertFields (SelectFields (locus alleles geneIds) (Ref row)) None (GenCC (GetField __uid_3316 (Ref row))))) (MakeStruct (__uid_3318 (ApplyAggOp Collect () ((SelectFields (geneIds GenCC) (SelectFields (locus alleles geneIds GenCC) (Ref row))))))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop) (Ref va)) None (GenCC (ToArray (StreamMap __uid_3320 (ToStream False (GetField __uid_3318 (GetField __uid_3319 (Ref va)))) (GetField GenCC (Ref __uid_3320))))))) (Let __cse_3 (GetField alleles (Ref va)) (Let __cse_4 (GetField locus (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC) (Ref va)) None (__uid_3321 (ArraySort __uid_3334 __uid_3335 (ToStream False (ToArray (StreamFlatMap __uid_3332 (ToStream False (ToArray (StreamFilter __uid_3322 (ToStream False (ToArray (StreamRange 15192 False (I32 1) (ArrayLen (CastToArray (Ref __cse_3))) (I32 1)))) (ApplyComparisonOp `!=` (Apply 15193 indexArray () String (Ref __cse_3) (Ref __uid_3322)) (Str "*"))))) (ToStream False (Let __uid_3333 (Apply 15205 min_rep () Struct{locus:Locus(GRCh38),alleles:Array[String]} (Ref __cse_4) (MakeArray Array[String] (Apply 15203 indexArray () String (Ref __cse_3) (I32 0)) (Apply 15204 indexArray () String (Ref __cse_3) (Ref __uid_3332)))) (If (ApplyComparisonOp `!=` (GetField locus (Ref __uid_3333)) (Ref __cse_4)) (MakeArray Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}] (MakeStruct (alleles (GetField alleles (Ref __uid_3333))) (locus (GetField locus (Ref __uid_3333))) (a_index (Ref __uid_3332)) (was_split (ApplyComparisonOp `>` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2))))) (NA Array[Struct{alleles:Array[String],locus:Locus(GRCh38),a_index:Int32,was_split:Boolean}]))))))) (If (IsNA (Ref __uid_3334)) (False) (If (IsNA (Ref __uid_3335)) (True) (If (False) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3335) (Ref __uid_3334)) (I32 0)) (ApplyComparisonOp `<` (ApplyComparisonOp Compare (Ref __uid_3334) (Ref __uid_3335)) (I32 0))))))))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Let __uid_3336 (GetField __uid_3321 (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC __uid_3321) (Ref va)) None (locus (GetField locus (Ref __uid_3336))) (alleles (GetField alleles (Ref __uid_3336))) (a_index (GetField a_index (Ref __uid_3336))) (was_split (GetField was_split (Ref __uid_3336))) (old_locus (GetField locus (Ref va))) (old_alleles (GetField alleles (Ref va))))))))) (Let __cse_5 (GetField vep (Ref va)) (Let __cse_6 (GetField a_index (Ref va)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split old_locus old_alleles) (Ref va)) None (vep (InsertFields (Ref __cse_5) None (intergenic_consequences (ToArray (StreamFilter __uid_3337 (ToStream False (GetField intergenic_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3337)) (Ref __cse_6))))) (motif_feature_consequences (ToArray (StreamFilter __uid_3338 (ToStream False (GetField motif_feature_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3338)) (Ref __cse_6))))) (regulatory_feature_consequences (ToArray (StreamFilter __uid_3339 (ToStream False (GetField regulatory_feature_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3339)) (Ref __cse_6))))) (transcript_consequences (ToArray (StreamFilter __uid_3340 (ToStream False (GetField transcript_consequences (Ref __cse_5))) (ApplyComparisonOp `==` (GetField allele_num (Ref __uid_3340)) (Ref __cse_6))))))))))) (Let __cse_10 (GetField a_index (Ref va)) (Let __cse_9 (If (ApplyUnaryPrimOp `!` (IsNA (GetField PL (Ref g)))) (ToArray (StreamMap __uid_3342 (ToStream False (ToArray (StreamRange 15210 False (I32 0) (I32 3) (I32 1)))) (Apply 15217 min () Int32 (ToArray (StreamFilter __uid_3345 (ToStream False (ToArray (StreamMap __uid_3344 (ToStream False (ToArray (StreamFilter __uid_3343 (ToStream False (ToArray (StreamRange 15212 False (I32 0) (Apply 15211 triangle () Int32 (ArrayLen (CastToArray (GetField old_alleles (Ref va))))) (I32 1)))) (ApplyComparisonOp `==` (Apply 15215 unphasedDiploidGtIndex () Int32 (Apply 15214 downcode () Call (Apply 15213 UnphasedDiploidGtIndexCall () Call (Ref __uid_3343)) (GetField a_index (Ref va)))) (Ref __uid_3342))))) (Apply 15216 indexArray () Int32 (GetField PL (Ref g)) (Ref __uid_3344))))) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3345)))))))) (NA Array[Int32])) (InsertFields (SelectFields (AD DP GQ GT MIN_DP PGT PID PL PS RGQ SB) (Ref g)) None (GT (Apply 15206 downcode () Call (GetField GT (Ref g)) (Ref __cse_10))) (DP (GetField DP (Ref g))) (AD (If (ApplyUnaryPrimOp `!` (IsNA (GetField AD (Ref g)))) (Let __cse_7 (GetField AD (Ref g)) (Let __cse_8 (GetField a_index (Ref va)) (MakeArray Array[Int32] (ApplyBinaryPrimOp `-` (Apply 15207 sum () Int32 (ToArray (StreamFilter __uid_3341 (ToStream False (Ref __cse_7)) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3341)))))) (Apply 15208 indexArray () Int32 (Ref __cse_7) (Ref __cse_8))) (Apply 15209 indexArray () Int32 (Ref __cse_7) (Ref __cse_8))))) (NA Array[Int32]))) (PL (Ref __cse_9)) (GQ (Coalesce (Apply 15218 gqFromPL () Int32 (Ref __cse_9)) (GetField GQ (Ref g)))) (PGT (Apply 15219 downcode () Call (GetField PGT (Ref g)) (Ref __cse_10))) (PID (GetField PID (Ref g))))))) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (aIndex (GetField aIndex (Ref va))) (AC (GetField AC (Ref va))) (AF (GetField AF (Ref va))) (alt (GetField alt (Ref va))) (AN (GetField AN (Ref va))) (cadd (GetField cadd (Ref va))) (clinvar (GetField clinvar (Ref va))) (codingGeneIds (GetField codingGeneIds (Ref va))) (contig (GetField contig (Ref va))) (dbnsfp (GetField dbnsfp (Ref va))) (docId (GetField docId (Ref va))) (domains (GetField domains (Ref va))) (eigen (GetField eigen (Ref va))) (end (GetField end (Ref va))) (exac (GetField exac (Ref va))) (filters (GetField filters (Ref va))) (g1k (GetField g1k (Ref va))) (geneIds (GetField geneIds (Ref va))) (geno2mp (GetField geno2mp (Ref va))) (genotypes (GetField genotypes (Ref va))) (gnomad_exome_coverage (GetField gnomad_exome_coverage (Ref va))) (gnomad_exomes (GetField gnomad_exomes (Ref va))) (gnomad_genome_coverage (GetField gnomad_genome_coverage (Ref va))) (gnomad_genomes (GetField gnomad_genomes (Ref va))) (mainTranscript (GetField mainTranscript (Ref va))) (mpc (GetField mpc (Ref va))) (originalAltAlleles (GetField originalAltAlleles (Ref va))) (pos (GetField pos (Ref va))) (primate_ai (GetField primate_ai (Ref va))) (ref (GetField ref (Ref va))) (rg37_locus (GetField rg37_locus (Ref va))) (rsid (GetField rsid (Ref va))) (samples_ab (GetField samples_ab (Ref va))) (samples_gq (GetField samples_gq (Ref va))) (samples_no_call (GetField samples_no_call (Ref va))) (samples_num_alt (GetField samples_num_alt (Ref va))) (sortedTranscriptConsequences (GetField sortedTranscriptConsequences (Ref va))) (splice_ai (GetField splice_ai (Ref va))) (start (GetField start (Ref va))) (topmed (GetField topmed (Ref va))) (transcriptConsequenceTerms (GetField transcriptConsequenceTerms (Ref va))) (transcriptIds (GetField transcriptIds (Ref va))) (variantId (GetField variantId (Ref va))) (vep (GetField vep (Ref va))) (wasSplit (GetField wasSplit (Ref va))) (xpos (GetField xpos (Ref va))) (xstart (GetField xstart (Ref va))) (xstop (GetField xstop (Ref va))) (GenCC (GetField GenCC (Ref va))) (a_index (GetField a_index (Ref va))) (was_split (GetField was_split (Ref va))) (old_locus (GetField old_locus (Ref va))) (old_alleles (GetField old_alleles (Ref va)))))) (AggLet __cse_11 False (GetField GT (Ref g)) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split) (Ref va)) None (variant_qc (Let __uid_3352 (MakeStruct (n_called (ApplyAggOp Sum () ((Apply 15234 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __cse_11))))))) (n_not_called (ApplyAggOp Sum () ((Apply 15235 toInt64 () Int64 (IsNA (Ref __cse_11)))))) (n_filtered (ApplyBinaryPrimOp `-` (Apply 15236 toInt64 () Int64 (Ref n_cols)) (ApplyAggOp Count () ()))) (call_stats (ApplyAggOp CallStats ((ArrayLen (CastToArray (GetField alleles (Ref va))))) ((Ref __cse_11))))) (Let __cse_18 (GetField call_stats (Ref __uid_3352)) (Let __cse_22 (GetField homozygote_count (Ref __cse_18)) (Let __cse_19 (GetField n_called (Ref __uid_3352)) (Let __cse_20 (GetField n_not_called (Ref __uid_3352)) (Let __cse_21 (GetField n_filtered (Ref __uid_3352)) (Let __uid_3353 (If (ApplyComparisonOp `==` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2)) (Let __cse_12 (GetField call_stats (Ref __uid_3352)) (Let __cse_13 (GetField homozygote_count (Ref __cse_12)) (Apply 15241 hardy_weinberg_test () Struct{het_freq_hwe:Float64,p_value:Float64} (Apply 15237 indexArray () Int32 (Ref __cse_13) (I32 0)) (ApplyBinaryPrimOp `-` (Apply 15238 indexArray () Int32 (GetField AC (Ref __cse_12)) (I32 1)) (ApplyBinaryPrimOp `*` (I32 2) (Apply 15239 indexArray () Int32 (Ref __cse_13) (I32 1)))) (Apply 15240 indexArray () Int32 (Ref __cse_13) (I32 1))))) (NA Struct{het_freq_hwe:Float64,p_value:Float64})) (MakeStruct (dp_stats (SelectFields (mean stdev min max) (AggLet __uid_agg3346 False (Apply 15220 toFloat64 () Float64 (GetField DP (Ref g))) (Let __uid_3347 (MakeStruct (n_def (ApplyAggOp Sum () ((Apply 15221 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_agg3346))))))) (sum (ApplyAggOp Sum () ((Ref __uid_agg3346)))) (sumsq (ApplyAggOp Sum () ((Apply 15223 pow () Float64 (Ref __uid_agg3346) (Apply 15222 toFloat64 () Float64 (I32 2)))))) (min (ApplyAggOp Min () ((Ref __uid_agg3346)))) (max (ApplyAggOp Max () ((Ref __uid_agg3346))))) (Let __cse_14 (GetField sum (Ref __uid_3347)) (Let __cse_15 (GetField n_def (Ref __uid_3347)) (Let __uid_3348 (ApplyBinaryPrimOp `/` (Ref __cse_14) (Apply 15224 toFloat64 () Float64 (Ref __cse_15))) (MakeStruct (mean (Ref __uid_3348)) (stdev (Apply 15226 sqrt () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (GetField sumsq (Ref __uid_3347)) (ApplyBinaryPrimOp `*` (Ref __uid_3348) (Ref __cse_14))) (Apply 15225 toFloat64 () Float64 (Ref __cse_15))))) (min (GetField min (Ref __uid_3347))) (max (GetField max (Ref __uid_3347))) (n (Ref __cse_15)) (sum (Ref __cse_14)))))))))) (gq_stats (SelectFields (mean stdev min max) (AggLet __uid_agg3349 False (Apply 15227 toFloat64 () Float64 (GetField GQ (Ref g))) (Let __uid_3350 (MakeStruct (n_def (ApplyAggOp Sum () ((Apply 15228 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_agg3349))))))) (sum (ApplyAggOp Sum () ((Ref __uid_agg3349)))) (sumsq (ApplyAggOp Sum () ((Apply 15230 pow () Float64 (Ref __uid_agg3349) (Apply 15229 toFloat64 () Float64 (I32 2)))))) (min (ApplyAggOp Min () ((Ref __uid_agg3349)))) (max (ApplyAggOp Max () ((Ref __uid_agg3349))))) (Let __cse_16 (GetField sum (Ref __uid_3350)) (Let __cse_17 (GetField n_def (Ref __uid_3350)) (Let __uid_3351 (ApplyBinaryPrimOp `/` (Ref __cse_16) (Apply 15231 toFloat64 () Float64 (Ref __cse_17))) (MakeStruct (mean (Ref __uid_3351)) (stdev (Apply 15233 sqrt () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (GetField sumsq (Ref __uid_3350)) (ApplyBinaryPrimOp `*` (Ref __uid_3351) (Ref __cse_16))) (Apply 15232 toFloat64 () Float64 (Ref __cse_17))))) (min (GetField min (Ref __uid_3350))) (max (GetField max (Ref __uid_3350))) (n (Ref __cse_17)) (sum (Ref __cse_16)))))))))) (AC (GetField AC (Ref __cse_18))) (AF (GetField AF (Ref __cse_18))) (AN (GetField AN (Ref __cse_18))) (homozygote_count (Ref __cse_22)) (call_rate (ApplyBinaryPrimOp `/` (Apply 15242 toFloat64 () Float64 (Ref __cse_19)) (Apply 15243 toFloat64 () Float64 (ApplyBinaryPrimOp `+` (ApplyBinaryPrimOp `+` (Ref __cse_19) (Ref __cse_20)) (Ref __cse_21))))) (n_called (Ref __cse_19)) (n_not_called (Ref __cse_20)) (n_filtered (Ref __cse_21)) (n_het (ApplyBinaryPrimOp `-` (Ref __cse_19) (Apply 15245 toInt64 () Int64 (Apply 15244 sum () Int32 (ToArray (StreamFilter __uid_3354 (ToStream False (Ref __cse_22)) (ApplyUnaryPrimOp `!` (IsNA (Ref __uid_3354))))))))) (n_non_ref (ApplyBinaryPrimOp `-` (Ref __cse_19) (Apply 15247 toInt64 () Int64 (Apply 15246 indexArray () Int32 (Ref __cse_22) (I32 0))))) (het_freq_hwe (GetField het_freq_hwe (Ref __uid_3353))) (p_value_hwe (GetField p_value (Ref __uid_3353))))))))))))))) (Let __cse_23 (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)) (Let __cse_26 (If (Apply 15251 land () Boolean (ApplyComparisonOp `>=` (Ref __cse_23) (Apply 15249 toFloat64 () Float64 (I32 0))) (ApplyComparisonOp `<=` (Ref __cse_23) (Apply 15250 toFloat64 () Float64 (I32 1)))) (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)) (Die Float64 15254 (Apply 15253 concat () String (Str "de_novo: expect 0 <= pop_frequency_prior <= 1, found ") (Apply 15252 str () String (Apply 15248 indexArray () Float64 (GetField AF (GetField variant_qc (Ref va))) (I32 1)))))) (AggLet __cse_25 False (GetField GT (Ref g)) (Let __cse_24 (ApplyAggOp Sum () ((Apply 15256 toInt64 () Int64 (Apply 15255 nNonRefAlleles () Int32 (Ref __cse_25))))) (InsertFields (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split variant_qc) (Ref va)) None (__prior (Ref __cse_26)) (__alt_alleles (Ref __cse_24)) (__site_freq (Apply 15261 max_ignore_missing () Float64 (Apply 15260 max_ignore_missing () Float64 (ApplyBinaryPrimOp `/` (ApplyBinaryPrimOp `-` (Ref __cse_24) (Apply 15259 toInt64 () Int64 (I32 1))) (ApplyBinaryPrimOp `*` (Apply 15258 toInt64 () Int64 (I32 2)) (ApplyAggOp Sum () ((Apply 15257 toInt64 () Int64 (ApplyUnaryPrimOp `!` (IsNA (Ref __cse_25)))))))) (Ref __cse_26)) (F64 3.3333333333333333e-06))))))))) (If (ApplyComparisonOp `==` (ArrayLen (CastToArray (GetField alleles (Ref va)))) (I32 2)) (SelectFields (locus alleles aIndex AC AF alt AN cadd clinvar codingGeneIds contig dbnsfp docId domains eigen end exac filters g1k geneIds geno2mp genotypes gnomad_exome_coverage gnomad_exomes gnomad_genome_coverage gnomad_genomes mainTranscript mpc originalAltAlleles pos primate_ai ref rg37_locus rsid samples_ab samples_gq samples_no_call samples_num_alt sortedTranscriptConsequences splice_ai start topmed transcriptConsequenceTerms transcriptIds variantId vep wasSplit xpos xstart xstop GenCC a_index was_split variant_qc __prior __alt_alleles __site_freq) (Ref va)) (Die Struct{locus:Locus(GRCh38),alleles:Array[String],aIndex:Int32,AC:Int32,AF:Float64,alt:String,AN:Int32,cadd:Struct{PHRED:Float32},clinvar:Struct{allele_id:Int32,clinical_significance:String,gold_stars:Int32},codingGeneIds:Set[String],contig:String,dbnsfp:Struct{SIFT_pred:String,Polyphen2_HVAR_pred:String,MutationTaster_pred:String,FATHMM_pred:String,MetaSVM_pred:String,REVEL_score:String,GERP_RS:String,phastCons100way_vertebrate:String},docId:String,domains:Set[String],eigen:Struct{Eigen_phred:Float64},end:Int32,exac:Struct{AF_POPMAX:Float64,AF:Float64,AC_Adj:Int32,AC_Het:Int32,AC_Hom:Int32,AC_Hemi:Int32,AN_Adj:Int32},filters:Set[String],g1k:Struct{AC:Int32,AF:Float64,AN:Int32,POPMAX_AF:Float64},geneIds:Set[String],geno2mp:Struct{HPO_Count:Int32},genotypes:Array[Struct{num_alt:Int32,gq:Int32,ab:Float64,dp:Float64,sample_id:String}],gnomad_exome_coverage:Float64,gnomad_exomes:Struct{AF:Float64,AN:Int32,AC:Int32,FAF_AF:Float64,AF_POPMAX_OR_GLOBAL:Float64,Hom:Int32,Hemi:Int32},gnomad_genome_coverage:Float64,gnomad_genomes:Struct{AF:Float64,AN:Int32,AC:Int32,FAF_AF:Float64,AF_POPMAX_OR_GLOBAL:Float64,Hom:Int32,Hemi:Int32},mainTranscript:Struct{biotype:String,canonical:Int32,category:String,cdna_start:Int32,cdna_end:Int32,codons:String,gene_id:String,gene_symbol:String,hgvs:String,hgvsc:String,major_consequence:String,major_consequence_rank:Int32,transcript_id:String,amino_acids:String,domains:String,hgvsp:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,polyphen_prediction:String,protein_id:String,sift_prediction:String},mpc:Struct{MPC:String},originalAltAlleles:Array[String],pos:Int32,primate_ai:Struct{score:Float64},ref:String,rg37_locus:Locus(GRCh37),rsid:String,samples_ab:Struct{0_to_5:Set[String],5_to_10:Set[String],10_to_15:Set[String],15_to_20:Set[String],20_to_25:Set[String],25_to_30:Set[String],30_to_35:Set[String],35_to_40:Set[String],40_to_45:Set[String]},samples_gq:Struct{0_to_5:Set[String],5_to_10:Set[String],10_to_15:Set[String],15_to_20:Set[String],20_to_25:Set[String],25_to_30:Set[String],30_to_35:Set[String],35_to_40:Set[String],40_to_45:Set[String],45_to_50:Set[String],50_to_55:Set[String],55_to_60:Set[String],60_to_65:Set[String],65_to_70:Set[String],70_to_75:Set[String],75_to_80:Set[String],80_to_85:Set[String],85_to_90:Set[String],90_to_95:Set[String]},samples_no_call:Set[String],samples_num_alt:Struct{1:Set[String],2:Set[String]},sortedTranscriptConsequences:Array[Struct{biotype:String,canonical:Int32,cdna_start:Int32,cdna_end:Int32,codons:String,gene_id:String,gene_symbol:String,hgvsc:String,hgvsp:String,transcript_id:String,amino_acids:String,lof:String,lof_filter:String,lof_flags:String,lof_info:String,polyphen_prediction:String,protein_id:String,protein_start:Int32,sift_prediction:String,consequence_terms:Array[String],domains:Array[String],major_consequence:String,category:String,hgvs:String,major_consequence_rank:Int32,transcript_rank:Int32}],splice_ai:Struct{delta_score:Float32,splice_consequence:String},start:Int32,topmed:Struct{AC:Int32,AF:Float64,AN:Int32,Hom:Int32,Het:Int32},transcriptConsequenceTerms:Set[String],transcriptIds:Set[String],variantId:String,vep:Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,appris:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,tsl:Int32,uniparc:String,variant_allele:String}],variant_class:String},wasSplit:Boolean,xpos:Int64,xstart:Int64,xstop:Int64,GenCC:Array[Struct{gene_symbol:String,inheritance_class:String,LOEUF:Float64,missense:Float64}],a_index:Int32,was_split:Boolean,variant_qc:Struct{dp_stats:Struct{mean:Float64,stdev:Float64,min:Float64,max:Float64},gq_stats:Struct{mean:Float64,stdev:Float64,min:Float64,max:Float64},AC:Array[Int32],AF:Array[Float64],AN:Int32,homozygote_count:Array[Int32],call_rate:Float64,n_called:Int64,n_not_called:Int64,n_filtered:Int64,n_het:Int64,n_non_ref:Int64,het_freq_hwe:Float64,p_value_hwe:Float64},__prior:Float64,__alt_alleles:Int64,__site_freq:Float64} 15267 (Apply 15266 concat () String (Apply 15264 concat () String (Apply 15263 concat () String (Str "'de_novo' expects biallelic variants ('alleles' field of length 2), found ") (Apply 15262 str () String (GetField locus (Ref va)))) (Str ", ")) (Apply 15265 str () String (GetField alleles (Ref va))))))) (InsertFields (SelectFields (s) (SelectFields (s cmg_data) (Ref sa))) None)) (InsertFields (SelectFields () (SelectFields (gencodeVersion sourceFilePath genomeVersion sampleType hail_version) (Ref global))) None)) (SelectFields (s) (Ref sa)))) (InsertFields (SelectFields (s) (SelectFields (s) (Ref row))) None))))) (GetField s (Ref __uid_3356)))) | |
| ^ | |
| | |
| | |
| # Coding variants | |
| # identify novel variants | |
| novel_mt=mt.filter_rows |
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