<commit_before>addSnpEffSplitter()
addGeneAnnotator("in_omim", "data/omimgenes")
addGeneAnnotator("in_hgmd", "data/hgmdgenes")
addGeneAnnotator("in_cosmic", "data/cosmicgenes")
addGeneAnnotator("exclusion", "data/fajardogenes")
addVCFAnnotator("data/niehs95.indels.vcf.gz", "AF=NIEHSIAF")
addVCFAnnotator("data/niehs95.snps.vcf.gz", "AF=NIEHSAF")
addVCFAnnotator("data/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz",
    "AMR_AF,ASN_AF,AFR_AF,EUR_AF,AF=TGAF")
addVCFAnnotator("data/ncbiSNP135.vcf.gz", 
    "SCS,GMAF,CLN,PM,G5A,G5").setCopyID(true)
addVCFAnnotator("data/ESP5400.vcf.gz",
    "MAF=ESPMAF,GTS,EA_GTC,AA_GTC,FG,GM,AA,AAC,PP,CDP,CG,GS,CA,DP=ESPDP,GL=ESPGL")
addVCFAnnotator("data/Complete_Public_Genomes_54genomes_VQHIGH.vcf.gz",
    "AF=CG54AF").setAddChr(true).setRequirePass(true)
addTSVAnnotator("data/dbNSFP2.0b1_variant.gz",
    "22=SIFT,23=HDIV_SCORE,23=HDIV_PRED,25=HVAR_SCORE,26=HVAR_PRED," +
    "27=LRT_SCORE,28=LRT_PRED,29=MT_SCORE,30=MT_PRED,31=GERP_NR,32=GERP_RS," +
    "33=PHYLOP,36=LRT_OMEGA").checkRef(3).checkAlt(4)<commit_msg>HDIV typo<commit_after>addSnpEffSplitter()
addGeneAnnotator("in_omim", "data/omimgenes")
addGeneAnnotator("in_hgmd", "data/hgmdgenes")
addGeneAnnotator("in_cosmic", "data/cosmicgenes")
addGeneAnnotator("exclusion", "data/fajardogenes")
addVCFAnnotator("data/niehs95.indels.vcf.gz", "AF=NIEHSIAF")
addVCFAnnotator("data/niehs95.snps.vcf.gz", "AF=NIEHSAF")
addVCFAnnotator("data/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz",
    "AMR_AF,ASN_AF,AFR_AF,EUR_AF,AF=TGAF")
addVCFAnnotator("data/ncbiSNP135.vcf.gz", 
    "SCS,GMAF,CLN,PM,G5A,G5").setCopyID(true)
addVCFAnnotator("data/ESP5400.vcf.gz",
    "MAF=ESPMAF,GTS,EA_GTC,AA_GTC,FG,GM,AA,AAC,PP,CDP,CG,GS,CA,DP=ESPDP,GL=ESPGL")
addVCFAnnotator("data/Complete_Public_Genomes_54genomes_VQHIGH.vcf.gz",
    "AF=CG54AF").setAddChr(true).setRequirePass(true)
addTSVAnnotator("data/dbNSFP2.0b1_variant.gz",
    "22=SIFT,23=HDIV_SCORE,24=HDIV_PRED,25=HVAR_SCORE,26=HVAR_PRED," +
    "27=LRT_SCORE,28=LRT_PRED,29=MT_SCORE,30=MT_PRED,31=GERP_NR,32=GERP_RS," +
    "33=PHYLOP,36=LRT_OMEGA").checkRef(3).checkAlt(4)
{'fraction_non_alphanumeric': 0.17690875232774675, 'fraction_numerical': 0.054003724394785846, 'mean_word_length': 10.553763440860216, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2576829', 'n_tokens_mistral': 1171, 'n_tokens_neox': 1070, 'n_words': 50}