if ( ! this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO"); for (final String format : genotypeAttributeKeys) if ( ! this.header.hasFormatLine(format)) fieldIsMissingFromHeaderError(context, format, "FORMAT");
for (final Map.Entry<String, Object> field : context.getAttributes().entrySet()) { if (!this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO"); for (final String format : genotypeAttributeKeys) if ( ! this.header.hasFormatLine(format)) fieldIsMissingFromHeaderError(context, format, "FORMAT");
for (final Map.Entry<String, Object> field : context.getAttributes().entrySet()) { if (!this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO"); for (final String format : genotypeAttributeKeys) if ( ! this.header.hasFormatLine(format)) fieldIsMissingFromHeaderError(context, format, "FORMAT");
private String getFilterString(final VariantContext vc) { if (vc.isFiltered()) { for (final String filter : vc.getFilters()) { if (!this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER"); } return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())); } else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4; else return VCFConstants.UNFILTERED; }
private String getFilterString(final VariantContext vc) { if (vc.isFiltered()) { for (final String filter : vc.getFilters()) { if (!this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER"); } return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())); } else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4; else return VCFConstants.UNFILTERED; }
private String getFilterString(final VariantContext vc) { if (vc.isFiltered()) { for (final String filter : vc.getFilters()) { if ( ! this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER"); } return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())); } else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4; else return VCFConstants.UNFILTERED; }