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lines changed Original file line number Diff line number Diff line change @@ -19,12 +19,17 @@ Changes affecting the whole of bcftools, or multiple commands:
1919 FORMAT/AD[0:GT] > 10 .. same as above, but in the first sample
2020 sSUM(FORMAT/AD[GT]) > 20 .. require total sample depth bigger than 20
2121
22+ * The commands `consensus -H` and `+split-vep -H`
23+
24+ - Drop unnecessary leading space in the first header column and newly print `#[1]columnName`
25+ instead of the previous `# [1]columnName` (#1856)
26+
2227
2328Changes affecting specific commands:
2429
2530* bcftools +allele-length
2631
27- - fix overflow for indels longer than 512bp and aggregate alleles equal or larger than
32+ - Fix overflow for indels longer than 512bp and aggregate alleles equal or larger than
2833 that in the same bin (#1837)
2934
3035* bcftools annotate
Original file line number Diff line number Diff line change 11/* convert.c -- functions for converting between VCF/BCF and related formats.
22
3- Copyright (C) 2013-2022 Genome Research Ltd.
3+ Copyright (C) 2013-2023 Genome Research Ltd.
44
55 Author: Petr Danecek <[email protected] > 66
@@ -1568,7 +1568,7 @@ int convert_header(convert_t *convert, kstring_t *str)
15681568 if ( i != convert -> nfmt )
15691569 return str -> l - l_ori ;
15701570
1571- kputs ( "# " , str );
1571+ kputc ( '#' , str );
15721572 for (i = 0 ; i < convert -> nfmt ; i ++ )
15731573 {
15741574 // Genotype fields
Original file line number Diff line number Diff line change 1- # [1]POS [2]Allele [3]Consequence [4]IMPACT [5]SYMBOL [6]Gene [7]Feature_type [8]Feature [9]BIOTYPE [10]EXON [11]INTRON [12]HGVSc [13]HGVSp [14]cDNA_position [15]CDS_position [16]Protein_position [17]Amino_acids [18]Codons [19]Existing_variation [20]ALLELE_NUM [21]DISTANCE [22]STRAND [23]FLAGS [24]VARIANT_CLASS [25]SYMBOL_SOURCE [26]HGNC_ID [27]CANONICAL [28]TSL [29]APPRIS [30]CCDS [31]ENSP [32]SWISSPROT [33]TREMBL [34]UNIPARC [35]SOURCE [36]GENE_PHENO [37]SIFT [38]PolyPhen [39]DOMAINS [40]miRNA [41]HGVS_OFFSET [42]AF [43]AFR_AF [44]AMR_AF [45]EAS_AF [46]EUR_AF [47]SAS_AF [48]AA_AF [49]EA_AF [50]gnomAD_AF [51]gnomAD_AFR_AF [52]gnomAD_AMR_AF [53]gnomAD_ASJ_AF [54]gnomAD_EAS_AF [55]gnomAD_FIN_AF [56]gnomAD_NFE_AF [57]gnomAD_OTH_AF [58]gnomAD_SAS_AF [59]MAX_AF [60]MAX_AF_POPS [61]CLIN_SIG [62]SOMATIC [63]PHENO [64]PUBMED [65]MOTIF_NAME [66]MOTIF_POS [67]HIGH_INF_POS [68]MOTIF_SCORE_CHANGE [69]LoF [70]LoF_filter [71]LoF_flags [72]LoF_info [73]CADD_PHRED [74]CADD_RAW [75]gnomAD2.1 [76]gnomAD2.1_AF_raw [77]gnomAD2.1_AF_popmax [78]gnomAD2.1_AF_afr [79]gnomAD2.1_AF_amr [80]gnomAD2.1_AF_asj [81]gnomAD2.1_AF_eas [82]gnomAD2.1_AF_fin [83]gnomAD2.1_AF_nfe [84]gnomAD2.1_AF_oth [85]gnomAD2.1_AF_sas
1+ #[1]POS [2]Allele [3]Consequence [4]IMPACT [5]SYMBOL [6]Gene [7]Feature_type [8]Feature [9]BIOTYPE [10]EXON [11]INTRON [12]HGVSc [13]HGVSp [14]cDNA_position [15]CDS_position [16]Protein_position [17]Amino_acids [18]Codons [19]Existing_variation [20]ALLELE_NUM [21]DISTANCE [22]STRAND [23]FLAGS [24]VARIANT_CLASS [25]SYMBOL_SOURCE [26]HGNC_ID [27]CANONICAL [28]TSL [29]APPRIS [30]CCDS [31]ENSP [32]SWISSPROT [33]TREMBL [34]UNIPARC [35]SOURCE [36]GENE_PHENO [37]SIFT [38]PolyPhen [39]DOMAINS [40]miRNA [41]HGVS_OFFSET [42]AF [43]AFR_AF [44]AMR_AF [45]EAS_AF [46]EUR_AF [47]SAS_AF [48]AA_AF [49]EA_AF [50]gnomAD_AF [51]gnomAD_AFR_AF [52]gnomAD_AMR_AF [53]gnomAD_ASJ_AF [54]gnomAD_EAS_AF [55]gnomAD_FIN_AF [56]gnomAD_NFE_AF [57]gnomAD_OTH_AF [58]gnomAD_SAS_AF [59]MAX_AF [60]MAX_AF_POPS [61]CLIN_SIG [62]SOMATIC [63]PHENO [64]PUBMED [65]MOTIF_NAME [66]MOTIF_POS [67]HIGH_INF_POS [68]MOTIF_SCORE_CHANGE [69]LoF [70]LoF_filter [71]LoF_flags [72]LoF_info [73]CADD_PHRED [74]CADD_RAW [75]gnomAD2.1 [76]gnomAD2.1_AF_raw [77]gnomAD2.1_AF_popmax [78]gnomAD2.1_AF_afr [79]gnomAD2.1_AF_amr [80]gnomAD2.1_AF_asj [81]gnomAD2.1_AF_eas [82]gnomAD2.1_AF_fin [83]gnomAD2.1_AF_nfe [84]gnomAD2.1_AF_oth [85]gnomAD2.1_AF_sas
2214464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000423562 unprocessed_pseudogene 10/10 . ENST00000423562.1:n.1568T>A . 1568 . . . . rs546169444 1 . -1 . SNV HGNC 38034 . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . .
3314464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000438504 unprocessed_pseudogene 12/12 . ENST00000438504.2:n.1682T>A . 1682 . . . . rs546169444 1 . -1 . SNV HGNC 38034 YES . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . .
4414464 T downstream_gene_variant MODIFIER DDX11L1 ENSG00000223972 Transcript ENST00000456328 processed_transcript . . . . . . . . . rs546169444 1 55 1 . SNV HGNC 37102 YES . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . .
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