Property Detail

• static java.util.List<java.lang.String> MG_COLUMNS

  MGHA redefined column order and contents to have a lot of things not of interest to others, so have a separate mapping for them.

• static java.util.List<java.lang.String> SIMPLE_COLUMNS

• java.util.List<java.lang.String> altIds

  Recognised alternative identifiers for the sample

• java.lang.String analysisContact

• java.lang.String batch

  Id of batch in which the sample was sequenced

• java.util.List<java.util.Date> captureDates

• Consanguinity consanguinity

  Whether the sample is consanguinous

• float dnaConcentrationNg

  DNA quality in nanograms

• java.util.List<java.util.Date> dnaDates

• float dnaQuality

• float dnaQuantity

• Ethnicity ethnicity

• java.util.Map<java.lang.String, java.util.List<java.lang.String>> fileMappings

• java.util.Map files

  List of files containing data specific to this sample, indexed by file types: - fastq - coverage (output from coverageBed) - vcf - bam - cram

• java.util.Map<java.lang.String, java.lang.Integer> geneCategories

  List of genes prioritised for the sample

• java.lang.String institution

  Hospital or organization responsible for the patient from which the sample originated

• java.lang.String library

  The library

• java.util.List<java.lang.String> machineIds

• float meanCoverage

  Mean coverage as reported by sequencing provider

• java.lang.String pedigree

  The pedigree of the family

• java.lang.String sample

  Sample name

• SampleType sampleType

  Whether the sample type is normal or tumor

• java.lang.String sequencingContact

• java.util.List<java.util.Date> sequencingDates

• Sex sex

  The sex of the sample

• java.lang.String target

  Target (flagship) name

• java.lang.String variantsFile

Constructor Detail

• SampleInfo()

Method Detail

• static java.util.Map<java.lang.String, SampleInfo> fromFiles(java.util.List<java.lang.String> files, java.lang.String mask)

  Create a list of SampleInfo objects from provided files that contain sample information in the header data. @return

  Parameters:

  files

• static java.util.List<java.lang.String> getBAMSamples(java.lang.String fileName)

• static java.util.List<java.lang.String> getVCFSamples(java.lang.String fileName)

• void indexFileType(java.lang.String index, java.util.List<java.lang.String> endings)

• void indexFileTypes()

• static java.util.Date parseDate(java.lang.String dateValue)

• static java.util.Map<java.lang.String, SampleInfo> parse_mg_sample_info(java.lang.String fileName)

  Parse the given file to extract sample info, where the file is in the extended Melbourne Genomics Health Alliance format. @return

  Parameters:

  fileName

• static java.util.Map<java.lang.String, SampleInfo> parse_sample_info(java.lang.String fileName)

  Parse sample info using auto-detection to determine if the format is MGHA extended format or simplified format. @return

  Parameters:

  fileName

• static java.util.Map<java.lang.String, SampleInfo> parse_sample_info(java.lang.String fileName, java.util.List columns)

  Parse the given file to extract sample information

  Returns:

  List of (Map) objects defining properties of each sample:

  sample name (sample),

  FastQ files (files),

  Name of flagship (target)

  Genes to be classed as high priority (genes)

• static java.util.List<java.lang.String> readSampleInfoLines(java.lang.String fileName)

• java.lang.String toString()

• java.lang.String toTsv(java.util.List<java.lang.String> columns, java.lang.String father, java.lang.String mother)

  Return a tab separated string compatible with the samples.txt file format, containing the details for this sample.

  @return

  Parameters:

  father - optional father id, if provided, will be output into the pedigree field

  mother - optional mother id, if provided, will be output into the pedigree field

• void validate()

  Validates that text fields are in the correct format.

  This format validation is specific to melbourne genomics.