{"id":"W2516950472","doi":"10.1186/s12859-016-1162-y","title":"BAMQL: a query language for extracting reads from BAM files","year":2016,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network; University of Toronto; Ontario Institute for Cancer Research","funders":"Prostate Cancer Canada; Government of Ontario; Canadian Institutes of Health Research; Genome Canada; Ontario Institute for Cancer Research; Terry Fox Research Institute; Movember Foundation; Johns Hopkins University","keywords":"Computer science; Web search query; Information retrieval; Database; Programming language; Search engine","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001308675,0.0001416812,0.0001362644,0.00002394491,0.0000820705,0.00002349235,0.0001521351,0.0001124224,0.00001675609],"category_scores_gemma":[0.000223675,0.00009835191,0.000103201,0.00002644909,0.00004594325,0.000002459318,0.0001018552,0.00002707897,0.00002960279],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001000034,"about_ca_system_score_gemma":0.00005219066,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000152829,"about_ca_topic_score_gemma":0.00006618816,"domain_scores_codex":[0.9992707,0.00001226852,0.0002705822,0.0001456722,0.00007169438,0.0002291326],"domain_scores_gemma":[0.9993422,0.0001142762,0.0001272672,0.0003056209,0.00005501951,0.00005560401],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001602353,0.00005574159,0.008940055,0.0001256336,0.0001830032,8.595244e-7,0.00124426,0.00004032332,0.9002755,0.0002208757,0.01436022,0.0743933],"study_design_scores_gemma":[0.005719613,0.001010877,0.03905346,0.0002714854,0.0002143511,0.00003168648,0.007294628,0.006359916,0.5762025,0.001607818,0.3602863,0.001947311],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.854928,0.001175916,0.1401729,0.0001234743,0.0003180837,0.0003494532,0.0007547995,0.00001586203,0.002161539],"genre_scores_gemma":[0.7271733,0.0003844888,0.2695611,0.0003812273,0.0007165243,0.00008114727,0.0002595641,0.00004016496,0.001402491],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3459261,"threshold_uncertainty_score":0.4010674,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0172345256371188,"score_gpt":0.252842834337511,"score_spread":0.2356083087003922,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}