Package org.broadinstitute.hellbender.tools.funcotator

Enum Class TranscriptSelectionMode

java.lang.Object
java.lang.Enum<TranscriptSelectionMode>
org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
All Implemented Interfaces:
Serializable, Comparable<TranscriptSelectionMode>, Constable
public enum TranscriptSelectionMode extends Enum<TranscriptSelectionMode>
The manner to select a single transcript from a set of transcripts to report as the "best" or main transcript. That is, the transcript that has the most information on it in the output.

  • Enum Constant Details

    • BEST_EFFECT

      public static final TranscriptSelectionMode BEST_EFFECT
      BEST_EFFECT Select a transcript to be reported with details with priority on effect according to the folowing list of selection criteria: Choose the transcript that is on the custom list specified by the user. If no list was specified, treat as if no transcripts were on the list (tie). In case of tie, choose the transcript that yields the variant classification highest on the variant classification rank list (see below). If still a tie, choose the transcript with highest level of curation. Note that this means lower number is better for level (see below). If still a tie, choose the transcript with the best appris annotation (see below). If still a tie, choose the transcript with the longest transcript sequence length. If still a tie, choose the first transcript, alphabetically. Levels of Curation: 1 (verified loci) 2 manually annotated loci 3 automatically annotated loci Variant Classification Scores (See GencodeFuncotation.VariantClassification as well): De_novo_Start_OutOfFrame 0 Nonsense_Mutation 0 Nonstop_Mutation 0 Missense_Mutation 1 De_novo_Start_InFrame 1 In_Frame_Del 1 In_Frame_Ins 1 Frame_Shift_Del 2 Frame_Shift_Ins 2 Frame_Shift_Sub 2 Start_Codon_SNP 3 Start_Codon_Del 3 Start_Codon_Ins 3 Start_Codon_DNP 3 Start_Codon_TNP 3 Start_Codon_ONP 3 Stop_Codon_SNP 3 Stop_Codon_Del 3 Stop_Codon_Ins 3 Stop_Codon_DNP 3 Stop_Codon_TNP 3 Stop_Codon_ONP 3 Splice_Site 4 Splice_Site_SNP 4 Splice_Site_Del 4 Splice_Site_Ins 4 Splice_Site_DNP 4 Splice_Site_TNP 4 Splice_Site_ONP 4 Splice_Site 4 miRNA 4 Silent 5 3UTR 6 5UTR 6 Intron 7 5Flank 8 3Flank 8 Non-coding_Transcript 9 IGR 20 TX-REF-MISMATCH 100 APPRIS Ranks (http://appris.bioinfo.cnio.es/): appris_principal appris_candidate_highest_score appris_candidate_longest_ccds appris_candidate_ccds appris_candidate_longest_seq appris_candidate_longest appris_candidate no appris tag present

    • CANONICAL

      public static final TranscriptSelectionMode CANONICAL
      CANONICAL Select a transcript to be reported with details with priority on canonical order according to the folowing list of selection criteria: Choose the transcript that is on the custom list specified by the user. If no list was specified, treat as if all transcripts were on the list (tie). In case of tie, choose the transcript with highest level of curation. Note that this means lower number is better for level (see below). If still a tie, choose the transcript that yields the variant classification highest on the variant classification rank list (see below). If still a tie, choose the transcript with the best appris annotation (see below). If still a tie, choose the transcript with the longest transcript sequence length. If still a tie, choose the first transcript, alphabetically. Levels of Curation: 1 (verified loci) 2 manually annotated loci 3 automatically annotated loci Variant Classification Scores (See GencodeFuncotation.VariantClassification as well): De_novo_Start_OutOfFrame 0 Nonsense_Mutation 0 Nonstop_Mutation 0 Missense_Mutation 1 De_novo_Start_InFrame 1 In_Frame_Del 1 In_Frame_Ins 1 Frame_Shift_Del 2 Frame_Shift_Ins 2 Frame_Shift_Sub 2 Start_Codon_SNP 3 Start_Codon_Del 3 Start_Codon_Ins 3 Start_Codon_DNP 3 Start_Codon_TNP 3 Start_Codon_ONP 3 Stop_Codon_SNP 3 Stop_Codon_Del 3 Stop_Codon_Ins 3 Stop_Codon_DNP 3 Stop_Codon_TNP 3 Stop_Codon_ONP 3 Splice_Site 4 Splice_Site_SNP 4 Splice_Site_Del 4 Splice_Site_Ins 4 Splice_Site_DNP 4 Splice_Site_TNP 4 Splice_Site_ONP 4 Splice_Site 4 miRNA 4 Silent 5 3UTR 6 5UTR 6 Intron 7 5Flank 8 3Flank 8 Non-coding_Transcript 9 IGR 20 TX-REF-MISMATCH 100 APPRIS Ranks (http://appris.bioinfo.cnio.es/): appris_principal appris_candidate_highest_score appris_candidate_longest_ccds appris_candidate_ccds appris_candidate_longest_seq appris_candidate_longest appris_candidate no appris tag present

    • ALL

      public static final TranscriptSelectionMode ALL
      Same as CANONICAL, but indicates that no transcripts should be dropped. Render all overlapping transcripts.

  • Method Details

    • values

      public static TranscriptSelectionMode[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static TranscriptSelectionMode valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum class has no constant with the specified name
      NullPointerException - if the argument is null

    • getComparator

      public abstract Comparator<GencodeFuncotation> getComparator(Set<String> userRequestedTranscripts)