bio-mocha/bcftools-1.14/mpileup.c

99     bcf_hdr_t *bcf_hdr;  member
570         flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);  in mpileup_reg()
584                 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);  in mpileup_reg()
732     conf->bcf_hdr = bcf_hdr_init("w");  in mpileup()
738         bcf_hdr_append(conf->bcf_hdr, conf->buf.s);  in mpileup()
744         bcf_hdr_append(conf->bcf_hdr, conf->buf.s);  in mpileup()
751         bcf_hdr_append(conf->bcf_hdr, conf->buf.s);  in mpileup()
760         bcf_hdr_append(conf->bcf_hdr, conf->buf.s);  in mpileup()
764 …bcf_hdr_append(conf->bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\…  in mpileup()
765 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the…  in mpileup()
766 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of…  in mpileup()
767 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of…  in mpileup()
768 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">"…  in mpileup()
770 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bi…  in mpileup()
774 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z t…  in mpileup()
775 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z t…  in mpileup()
776 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z t…  in mpileup()
777 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z …  in mpileup()
779 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SCBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z t…  in mpileup()
782 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test…  in mpileup()
783 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test…  in mpileup()
784 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test…  in mpileup()
785 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U tes…  in mpileup()
788 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=FS,Number=1,Type=Float,Description=\"Phred-scaled p-value…  in mpileup()
790 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U tes…  in mpileup()
791 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U tes…  in mpileup()
792 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U tes…  in mpileup()
793 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U te…  in mpileup()
795 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based m…  in mpileup()
796 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 re…  in mpileup()
797 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used…  in mpileup()
798 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used f…  in mpileup()
799 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-sc…  in mpileup()
801 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-q…  in mpileup()
803 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-q…  in mpileup()
805 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-…  in mpileup()
807 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-qu…  in mpileup()
809 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-…  in mpileup()
811 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled str…  in mpileup()
813 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths (…  in mpileup()
815 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths …  in mpileup()
817 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths …  in mpileup()
819 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=QS,Number=R,Type=Integer,Description=\"Phred-score alle…  in mpileup()
821 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic dept…  in mpileup()
823 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic dep…  in mpileup()
825 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SCR,Number=1,Type=Integer,Description=\"Number of soft-cl…  in mpileup()
827 …bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SCR,Number=1,Type=Integer,Description=\"Per-sample numb…  in mpileup()
829 …bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic dep…  in mpileup()
831         gvcf_update_header(conf->gvcf, conf->bcf_hdr);  in mpileup()
836         bcf_hdr_add_sample(conf->bcf_hdr, smpl[i]);  in mpileup()
837 …if ( bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr)!=0 ) error("[%s] Error: failed to write the header…  in mpileup()
851     conf->bc.bcf_hdr = conf->bcf_hdr;  in mpileup()
926     flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, NULL);  in mpileup()
934         bcf_hdr_destroy(conf->bcf_hdr);  in mpileup()