Skip to content

Fix non-deterministic field ordering in AnnotationSourceTSV annotation extraction #403

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
holmeso merged 3 commits into from
Mar 3, 2026
+32 −5
Merged

Fix non-deterministic field ordering in AnnotationSourceTSV annotation extraction #403

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0cd751f
Initial plan
Copilot Feb 27, 2026
d431245
fix: preserve user-requested field order in AnnotationSourceTSV by it…
Copilot Feb 27, 2026
623d911
test: add test verifying user-requested field order is preserved in a…
Copilot Mar 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,12 @@ public AnnotationSourceTSV(RecordReader<String> reader, int chrPositionInRecord,
if (headerNameAndPosition.isEmpty()) {
throw new IllegalArgumentException("Could not find requested fields (" + fieldNames + ") in header: " + headerLine);
}
// precompute arrays for fast extraction
this.fieldNames = headerNameAndPosition.keySet().toArray(new String[0]);
this.fieldPositions = new int[this.fieldNames.length];
for (int i = 0; i < this.fieldNames.length; i++) {
this.fieldPositions[i] = headerNameAndPosition.get(this.fieldNames[i]);
// precompute arrays for fast extraction, preserving user-requested field order
String[] requestedFields = fieldNames.split(",");
this.fieldNames = requestedFields;
this.fieldPositions = new int[requestedFields.length];
for (int i = 0; i < requestedFields.length; i++) {
this.fieldPositions[i] = headerNameAndPosition.get(requestedFields[i]);
}
}

Expand Down
26 changes: 26 additions & 0 deletions qannotate/test/au/edu/qimr/qannotate/nanno/AnnotationSourceTSVTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,32 @@ public void extractFieldsFromRecord() {

}

@Test
public void fieldOrderPreservedFromUserRequest() {
/*
* header has fields in order: alpha, beta, gamma
* user requests them in reverse: gamma,beta,alpha
* output should match user-requested order, not header order
*/
String header = "alpha\tbeta\tgamma";
String[] record = new String[]{"val_alpha", "val_beta", "val_gamma"};

Map<String, Integer> fieldsAndPositions = AnnotationSourceTSV.getHeaderNameAndPositions("gamma,beta,alpha", header);
assertEquals(2, fieldsAndPositions.get("gamma").intValue());
assertEquals(1, fieldsAndPositions.get("beta").intValue());
assertEquals(0, fieldsAndPositions.get("alpha").intValue());

// build arrays the same way the constructor does (using split order, not keyset order)
String[] requestedFields = "gamma,beta,alpha".split(",");
int[] positions = new int[requestedFields.length];
for (int i = 0; i < requestedFields.length; i++) {
positions[i] = fieldsAndPositions.get(requestedFields[i]);
}
// output must be in user-requested order: gamma, beta, alpha
assertEquals("gamma=val_gamma\tbeta=val_beta\talpha=val_alpha",
AnnotationSourceTSV.extractFieldsFromRecord(record, requestedFields, positions));
}

@Test
public void getHeaderNameAndPositions() {
List<String> headerLines = Arrays.asList(new String[] {"","#chr pos(1-based) ref alt aaref aaalt rs_dbSNP151 hg19_chr hg19_pos(1-based) hg18_chr hg18_pos(1-based) aapos genename Ensembl_geneid Ensembl_transcriptid Ensembl_proteinid Uniprot_acc Uniprot_entry HGVSc_ANNOVAR HGVSp_ANNOVAR HGVSc_snpEff HGVSp_snpEff HGVSc_VEP HGVSp_VEP APPRIS GENCODE_basic TSL VEP_canonicalcds_strand refcodon codonpos codon_degeneracy Ancestral_allele AltaiNeandertal Denisova VindijiaNeandertal SIFT_score SIFT_converted_rankscore SIFT_pred SIFT4G_score SIFT4G_converted_rankscore SIFT4G_pred Polyphen2_HDIV_score Polyphen2_HDIV_rankscore Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_rankscorePolyphen2_HVAR_pred LRT_score LRT_converted_rankscore LRT_pred LRT_Omega MutationTaster_score MutationTaster_converted_rankscore MutationTaster_pred MutationTaster_modelMutationTaster_AAE MutationAssessor_score MutationAssessor_rankscore MutationAssessor_pred FATHMM_score FATHMM_converted_rankscore FATHMM_pred PROVEAN_score PROVEAN_converted_rankscore PROVEAN_pred VEST4_score VEST4_rankscore MetaSVM_score MetaSVM_rankscore MetaSVM_pred MetaLR_score MetaLR_rankscore MetaLR_pred Reliability_index M-CAP_scoreM-CAP_rankscore M-CAP_pred REVEL_score REVEL_rankscore MutPred_score MutPred_rankscore MutPred_protID MutPred_AAchange MutPred_Top5features MVP_score MVP_rankscore MPC_score MPC_rankscore PrimateAI_score PrimateAI_rankscore PrimateAI_pred DEOGEN2_score DEOGEN2_rankscore DEOGEN2_pred BayesDel_addAF_score BayesDel_addAF_rankscore BayesDel_addAF_pred BayesDel_noAF_score BayesDel_noAF_rankscore BayesDel_noAF_pred ClinPred_score ClinPred_rankscore ClinPred_pred LIST-S2_score LIST-S2_rankscore LIST-S2_pred Aloft_Fraction_transcripts_affected Aloft_prob_Tolerant Aloft_prob_Recessive Aloft_prob_Dominant Aloft_pred Aloft_Confidence CADD_raw CADD_raw_rankscore CADD_phred CADD_raw_hg19CADD_raw_rankscore_hg19 CADD_phred_hg19 DANN_score DANN_rankscore fathmm-MKL_coding_score fathmm-MKL_coding_rankscore fathmm-MKL_coding_pred fathmm-MKL_coding_group fathmm-XF_coding_score fathmm-XF_coding_rankscore fathmm-XF_coding_pred Eigen-raw_coding Eigen-raw_coding_rankscore Eigen-phred_coding Eigen-PC-raw_coding Eigen-PC-raw_coding_rankscore Eigen-PC-phred_codingGenoCanyon_score GenoCanyon_rankscore integrated_fitCons_score integrated_fitCons_rankscore integrated_confidence_value GM12878_fitCons_score GM12878_fitCons_rankscore GM12878_confidence_value H1-hESC_fitCons_score H1-hESC_fitCons_rankscore H1-hESC_confidence_value HUVEC_fitCons_score HUVEC_fitCons_rankscore HUVEC_confidence_value LINSIGHT LINSIGHT_rankscore GERP++_NR GERP++_RS GERP++_RS_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore phyloP30way_mammalian phyloP30way_mammalian_rankscore phyloP17way_primate phyloP17way_primate_rankscore phastCons100way_vertebrate phastCons100way_vertebrate_rankscore phastCons30way_mammalian phastCons30way_mammalian_rankscore phastCons17way_primatephastCons17way_primate_rankscore SiPhy_29way_pi SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore bStatistic bStatistic_converted_rankscore 1000Gp3_AC 1000Gp3_AF 1000Gp3_AFR_AC1000Gp3_AFR_AF 1000Gp3_EUR_AC 1000Gp3_EUR_AF 1000Gp3_AMR_AC 1000Gp3_AMR_AF 1000Gp3_EAS_AC 1000Gp3_EAS_AF 1000Gp3_SAS_AC 1000Gp3_SAS_AF TWINSUK_AC TWINSUK_AF ALSPAC_AC ALSPAC_AFUK10K_AC UK10K_AF ESP6500_AA_AC ESP6500_AA_AF ESP6500_EA_AC ESP6500_EA_AF ExAC_AC ExAC_AF ExAC_Adj_AC ExAC_Adj_AF ExAC_AFR_AC ExAC_AFR_AF ExAC_AMR_AC ExAC_AMR_AFExAC_EAS_AC ExAC_EAS_AF ExAC_FIN_AC ExAC_FIN_AF ExAC_NFE_AC ExAC_NFE_AF ExAC_SAS_AC ExAC_SAS_AF ExAC_nonTCGA_AC ExAC_nonTCGA_AF ExAC_nonTCGA_Adj_AC ExAC_nonTCGA_Adj_AFExAC_nonTCGA_AFR_AC ExAC_nonTCGA_AFR_AF ExAC_nonTCGA_AMR_AC ExAC_nonTCGA_AMR_AF ExAC_nonTCGA_EAS_AC ExAC_nonTCGA_EAS_AF ExAC_nonTCGA_FIN_AC ExAC_nonTCGA_FIN_AF ExAC_nonTCGA_NFE_AC ExAC_nonTCGA_NFE_AF ExAC_nonTCGA_SAS_AC ExAC_nonTCGA_SAS_AF ExAC_nonpsych_AC ExAC_nonpsych_AF ExAC_nonpsych_Adj_AC ExAC_nonpsych_Adj_AF ExAC_nonpsych_AFR_AC ExAC_nonpsych_AFR_AF ExAC_nonpsych_AMR_AC ExAC_nonpsych_AMR_AF ExAC_nonpsych_EAS_AC ExAC_nonpsych_EAS_AF ExAC_nonpsych_FIN_AC ExAC_nonpsych_FIN_AF ExAC_nonpsych_NFE_AC ExAC_nonpsych_NFE_AFExAC_nonpsych_SAS_AC ExAC_nonpsych_SAS_AF gnomAD_exomes_flag gnomAD_exomes_AC gnomAD_exomes_AN gnomAD_exomes_AF gnomAD_exomes_nhomalt gnomAD_exomes_AFR_AC gnomAD_exomes_AFR_AN gnomAD_exomes_AFR_AF gnomAD_exomes_AFR_nhomalt gnomAD_exomes_AMR_AC gnomAD_exomes_AMR_AN gnomAD_exomes_AMR_AF gnomAD_exomes_AMR_nhomalt gnomAD_exomes_ASJ_AC gnomAD_exomes_ASJ_AN gnomAD_exomes_ASJ_AF gnomAD_exomes_ASJ_nhomalt gnomAD_exomes_EAS_AC gnomAD_exomes_EAS_AN gnomAD_exomes_EAS_AF gnomAD_exomes_EAS_nhomalt gnomAD_exomes_FIN_AC gnomAD_exomes_FIN_AN gnomAD_exomes_FIN_AF gnomAD_exomes_FIN_nhomalt gnomAD_exomes_NFE_AC gnomAD_exomes_NFE_AN gnomAD_exomes_NFE_AF gnomAD_exomes_NFE_nhomalt gnomAD_exomes_SAS_AC gnomAD_exomes_SAS_AN gnomAD_exomes_SAS_AF gnomAD_exomes_SAS_nhomalt gnomAD_exomes_POPMAX_AC gnomAD_exomes_POPMAX_AN gnomAD_exomes_POPMAX_AF gnomAD_exomes_POPMAX_nhomalt gnomAD_exomes_controls_AC gnomAD_exomes_controls_AN gnomAD_exomes_controls_AF gnomAD_exomes_controls_nhomalt gnomAD_exomes_controls_AFR_AC gnomAD_exomes_controls_AFR_AN gnomAD_exomes_controls_AFR_AF gnomAD_exomes_controls_AFR_nhomalt gnomAD_exomes_controls_AMR_AC gnomAD_exomes_controls_AMR_AN gnomAD_exomes_controls_AMR_AF gnomAD_exomes_controls_AMR_nhomalt gnomAD_exomes_controls_ASJ_AC gnomAD_exomes_controls_ASJ_AN gnomAD_exomes_controls_ASJ_AF gnomAD_exomes_controls_ASJ_nhomalt gnomAD_exomes_controls_EAS_AC gnomAD_exomes_controls_EAS_AN gnomAD_exomes_controls_EAS_AF gnomAD_exomes_controls_EAS_nhomalt gnomAD_exomes_controls_FIN_AC gnomAD_exomes_controls_FIN_AN gnomAD_exomes_controls_FIN_AF gnomAD_exomes_controls_FIN_nhomalt gnomAD_exomes_controls_NFE_AC gnomAD_exomes_controls_NFE_ANgnomAD_exomes_controls_NFE_AF gnomAD_exomes_controls_NFE_nhomalt gnomAD_exomes_controls_SAS_AC gnomAD_exomes_controls_SAS_AN gnomAD_exomes_controls_SAS_AF gnomAD_exomes_controls_SAS_nhomaltgnomAD_exomes_controls_POPMAX_AC gnomAD_exomes_controls_POPMAX_AN gnomAD_exomes_controls_POPMAX_AF gnomAD_exomes_controls_POPMAX_nhomalt gnomAD_genomes_flag gnomAD_genomes_ACgnomAD_genomes_AN gnomAD_genomes_AF gnomAD_genomes_nhomalt gnomAD_genomes_AFR_AC gnomAD_genomes_AFR_AN gnomAD_genomes_AFR_AF gnomAD_genomes_AFR_nhomalt gnomAD_genomes_AMR_AC gnomAD_genomes_AMR_AN gnomAD_genomes_AMR_AF gnomAD_genomes_AMR_nhomalt gnomAD_genomes_ASJ_AC gnomAD_genomes_ASJ_AN gnomAD_genomes_ASJ_AF gnomAD_genomes_ASJ_nhomalt gnomAD_genomes_EAS_AC gnomAD_genomes_EAS_AN gnomAD_genomes_EAS_AF gnomAD_genomes_EAS_nhomalt gnomAD_genomes_FIN_AC gnomAD_genomes_FIN_AN gnomAD_genomes_FIN_AF gnomAD_genomes_FIN_nhomalt gnomAD_genomes_NFE_AC gnomAD_genomes_NFE_AN gnomAD_genomes_NFE_AF gnomAD_genomes_NFE_nhomalt gnomAD_genomes_AMI_AC gnomAD_genomes_AMI_AN gnomAD_genomes_AMI_AF gnomAD_genomes_AMI_nhomalt gnomAD_genomes_SAS_AC gnomAD_genomes_SAS_AN gnomAD_genomes_SAS_AF gnomAD_genomes_SAS_nhomalt gnomAD_genomes_POPMAX_AC gnomAD_genomes_POPMAX_AN gnomAD_genomes_POPMAX_AF gnomAD_genomes_POPMAX_nhomalt clinvar_id clinvar_clnsig clinvar_trait clinvar_review clinvar_hgvs clinvar_var_source clinvar_MedGen_id clinvar_OMIM_id clinvar_Orphanet_id Interpro_domain GTEx_V8_gene GTEx_V8_tissueGeuvadis_eQTL_target_gene"});
Expand Down