{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.006976806,0.002481473,0.001514626,0.002263718,0.001375327,0.003400314,0.004266557,0.001783848,0.03560544],"category_scores_gemma":[0.01350933,0.001802136,0.001552509,0.002436227,0.001255363,0.004573593,0.004416487,0.002832611,0.02672083],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009322203,"about_ca_system_score_gemma":0.001970165,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002438856,"about_ca_topic_score_gemma":0.001825713,"domain_scores_codex":[0.9964058,0.0007634794,0.0006262657,0.0008120398,0.00113108,0.0002614635],"domain_scores_gemma":[0.9921337,0.004598648,0.0006451495,0.0009493273,0.001269621,0.0004034587],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.003415897,0.0003438672,0.008122421,0.009766342,0.0005165205,0.001727193,0.003209169,0.005641453,0.1300207,0.02294063,0.5823503,0.2319457],"study_design_scores_gemma":[0.0005918682,0.0004385867,0.005612438,0.0009439024,0.0001764359,0.002585978,0.001079355,0.05019175,0.1750883,0.04096634,0.7216555,0.0006694898],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.005148708,0.0006235539,0.5601314,0.0006659408,0.0001893115,0.0006237841,0.0670269,0.3605208,0.005069613],"genre_scores_gemma":[0.05418753,0.00104943,0.6189494,0.002319303,0.0002728469,0.002828392,0.1836224,0.1281992,0.008571578],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03560544,"threshold_uncertainty_score":0.119112,"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."}}