b952080d3da3a9e027da627804e32a08b17366d3,cnvlib/export.py,,,#,336

Before Change

// _____________________________________________________________________________

EXPORT_FORMATS = {
    "cdt": fmt_cdt,
    // "gct": fmt_gct,
    "jtv": fmt_jtv,
    // "vcf": fmt_vcf,
    "nexus-basic": export_nexus_basic,
    // "nexus-multi1": fmt_multi,
    "seg": export_seg,
    "freebayes": export_freebayes,
    "theta": export_theta,
}

After Change

// 3 12665100  . A <DUP>   14  PASS  IMPRECISE;SVTYPE=DUP;END=12686200;SVLEN=21100;CIPOS=-500,500;CIEND=-500,500   GT:GQ:CN:CNQ  ./.:0:3:16.2
// 4 18665128  . T <DUP:TANDEM>  11  PASS  IMPRECISE;SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10  GT:GQ:CN:CNQ  ./.:0:5:8.3

VCF_COLUMNS = ("//CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT")


def export_vcf(sample_fname, args):
    Convert segments to Variant Call Format.

Instances