Function reference • dracarys

All functions

BcftoolsStatsFile: BcftoolsStatsFile R6 Class

BclconvertReports: BclconvertReports R6 Class

FastqcMetricsFile: FastqcMetrics R6 Class

File: File R6 Class

FragmentLengthHistFile: FragmentLengthHistFile R6 Class

MappingMetricsFile: MappingMetricsFile R6 Class

MultiqcFile: MultiqcFile R6 Class

PcgrJsonFile: PcgrJson R6 Class

PcgrTiersFile: PcgrTiersFile R6 Class

PloidyEstimationMetricsFile: PloidyEstimationMetricsFile R6 Class

ReplayFile: ReplayFile R6 Class

SvMetricsFile: SvMetricsFile R6 Class

TimeMetricsFile: TimeMetricsFile R6 Class

TrimmerMetricsFile: TrimmerMetricsFile R6 Class

TsoAlignCollapseFusionCallerMetricsFile: TsoAlignCollapseFusionCallerMetricsFile R6 Class

TsoCombinedVariantOutputFile: TsoCombinedVariantOutputFile R6 Class

TsoCopyNumberVariantsVcfFile: TsoCopyNumberVariantsVcfFile R6 Class

TsoFragmentLengthHistFile: TsoFragmentLengthHistFile R6 Class

TsoFusionsCsvFile: TsoFusionsCsvFile R6 Class

TsoMergedSmallVariantsGenomeVcfFile: TsoMergedSmallVariantsGenomeVcfFile R6 Class

TsoMergedSmallVariantsVcfFile: TsoMergedSmallVariantsVcfFile R6 Class

TsoMsiFile: TsoMsiFile R6 Class

TsoSampleAnalysisResultsFile: TsoSampleAnalysisResultsFile R6 Class

TsoTargetRegionCoverageFile: TsoTargetRegionCoverageFile R6 Class

TsoTmbFile: TsoTmbFile R6 Class

TsoTmbTraceTsvFile: TsoTmbTraceTsvFile R6 Class

UmChordTsvFile: UmChordTsvFile R6 Class

UmHrdetectTsvFile: UmHrdetectTsvFile R6 Class

UmQcSumFile: UmQcSumFile R6 Class

UmSigsSnvFile: UmSigsSnvFile R6 Class

VCMetricsFile: VCMetricsFile R6 Class

WgsContigMeanCovFile: WgsContigMeanCovFile R6 Class

WgsCoverageMetricsFile: WgsCoverageMetricsFile R6 Class

WgsFineHistFile: WgsFineHistFile R6 Class

WgsHistFile: WgsHistFile R6 Class

bcftools_parse_vcf(): Parse VCF with bcftools

bcftools_parse_vcf_regions(): Parse VCF regions with bcftools

bclconvert_read_adaptermetrics(): BCLConvert Adapter Metrics

bclconvert_read_demultiplexstats(): BCLConvert Demultiplex Stats

bclconvert_read_indexhoppingcounts(): BCLConvert Index Hopping Counts

bclconvert_read_topunknownbarcodes(): BCLConvert Top Unknown Barcodes

date_log(): Print current timestamp for logging

dr_func_eval(): Evaluate dracarys Function

dr_gds_download(): dracarys GDS Download

dr_output_format_valid(): Output Format is Valid

dr_s3_download(): dracarys S3 Download

empty_tbl(): Create Empty Tibble Given Column Names

file_regex_getter(): Get dracarys DR_FILE_REGEX

gds_file_download(): GDS File Download via CLI

gds_file_download_api(): GDS File Download via API

gds_file_presignedurl(): GDS File Presigned URL

gds_files_list(): GDS Files List

gds_files_list_filter_relevant(): List Relevant Files In GDS Directory

gds_volumes_list(): List GDS Volumes

ica_token_validate(): Validate ICA access token

match_regex(): Match File to Regex

multiqc_column_map_append(): Append New MultiQC Workflow Columns

multiqc_date_fmt(): Format MultiQC Config Date

multiqc_parse_bargraph_plot(): MultiQC Extract Bar Graph Data

multiqc_parse_gen(): Parse MultiQC 'report_general_stats_data' JSON Element

multiqc_parse_plots(): Parse Plot Data from MultiQC JSON

multiqc_parse_raw(): Parse MultiQC 'report_saved_raw_data' JSON Element

multiqc_parse_raw_interop(): Parse Interop MultiQC 'report_saved_raw_data' JSON Element

multiqc_parse_xyline_plot(): MultiQC Extract XY Line Plot Data

multiqc_parse_xyline_plot_contig_cvg(): MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage

multiqc_tidy_json(): Tidy MultiQC JSON

rdf2tab(): Write Local R Dataframe to Spark-backed Table

read(<File>): Read File object

read(): Generic Reading

s3_files_list_filter_relevant(): List Relevant Files In AWS S3 Directory

s3_search(): Search AWS S3 Objects

session_info_kable(): Session Information Kable

time_metrics_process(): Process Multiple TimeMetricsFile Objects

umccr_tidy(): Tidy UMCCR Results