Merge pull request #56 from msk-access/develop

Bug fix for OR sign

R/compile_reads.R

@@ -109,7 +109,7 @@ compile_reads <- function(
       # fread(x) %>% filter(as.numeric(D_t_alt_count_fragment) > 0) %>% data.table()
       selectcolumns <- c("Hugo_Symbol","Entrez_Gene_Id","Center","NCBI_Build","Chromosome","Start_Position","End_Position","Strand","Variant_Classification","Variant_Type","Reference_Allele","Tumor_Seq_Allele1","Tumor_Seq_Allele2","dbSNP_RS","dbSNP_Val_Status","Tumor_Sample_Barcode","caller_Norm_Sample_Barcode","Match_Norm_Seq_Allele1","Match_Norm_Seq_Allele2","Tumor_Validation_Allele1","Tumor_Validation_Allele2","Match_Norm_Validation_Allele1","Match_Norm_Validation_Allele2","Verification_Status","Validation_Status","Mutation_Status","Sequencing_Phase","Sequence_Source","Validation_Method","Score","BAM_File","Sequencer","Tumor_Sample_UUID","Matched_Norm_Sample_UUID","HGVSc","HGVSp","HGVSp_Short","Transcript_ID","Exon_Number","caller_t_depth","caller_t_ref_count","caller_t_alt_count","caller_n_depth","caller_n_ref_count","caller_n_alt_count","all_effects","Allele","Gene","Feature","Feature_type","Consequence","cDNA_position","CDS_position","Protein_position","Amino_acids","Codons","Existing_variation","ALLELE_NUM","DISTANCE","STRAND_VEP","SYMBOL","SYMBOL_SOURCE","HGNC_ID","BIOTYPE","CANONICAL","CCDS","ENSP","SWISSPROT","TREMBL","UNIPARC","RefSeq","SIFT","PolyPhen","EXON","INTRON","DOMAINS","AF","AFR_AF","AMR_AF","ASN_AF","EAS_AF","EUR_AF","SAS_AF","AA_AF","EA_AF","CLIN_SIG","SOMATIC","PUBMED","MOTIF_NAME","MOTIF_POS","HIGH_INF_POS","MOTIF_SCORE_CHANGE","IMPACT","PICK","VARIANT_CLASS","TSL","HGVS_OFFSET","PHENO","MINIMISED","ExAC_AF","ExAC_AF_AFR","ExAC_AF_AMR","ExAC_AF_EAS","ExAC_AF_FIN","ExAC_AF_NFE","ExAC_AF_OTH","ExAC_AF_SAS","GENE_PHENO","FILTER","flanking_bps","variant_id","variant_qual","ExAC_AF_Adj","ExAC_AC_AN_Adj","ExAC_AC_AN","ExAC_AC_AN_AFR","ExAC_AC_AN_AMR","ExAC_AC_AN_EAS","ExAC_AC_AN_FIN","ExAC_AC_AN_NFE","ExAC_AC_AN_OTH","ExAC_AC_AN_SAS","ExAC_FILTER","gnomAD_AF","gnomAD_AFR_AF","gnomAD_AMR_AF","gnomAD_ASJ_AF","gnomAD_EAS_AF","gnomAD_FIN_AF","gnomAD_NFE_AF","gnomAD_OTH_AF","gnomAD_SAS_AF","CallMethod","VCF_POS","VCF_REF","VCF_ALT","hotspot_whitelist","Status","D_t_alt_count_fragment","D_t_ref_count_fragment","D_t_vaf_fragment","SD_t_alt_count_fragment","SD_t_ref_count_fragment","SD_t_vaf_fragment","Matched_Norm_Sample_Barcode","Matched_Norm_Bamfile","n_alt_count_fragment","n_ref_count_fragment","n_vaf_fragment")
       if("Status" %in% names(fread(x))){
-          fread(x) %>% select(one_of(selectcolumns)) %>% subset((Status == "") || (is.na(Status)))
+          fread(x) %>% select(one_of(selectcolumns)) %>% subset((Status == "") | (is.na(Status)))
       } else {
           fread(x) %>% select(one_of(selectcolumns))
       }