Class SnpEffPredictorFactory

Method Details

• add

  protected void add(Cds cds)

• add

  protected void add(Chromosome chromo)

• add

  protected Exon add(Exon exon)

  Add an exon

  Parameters:

  exon -

  Returns:

  exon added. Note: If the exon exists with the same ID, return old exon. If exon exists with same ID and same coordiates, add a new exon with different ID.

• add

  protected void add(Gene gene)

  Add a Gene

• add

  protected void add(Marker marker)

  Add a generic Marker

• add

  protected void add(Transcript tr)

  Add a transcript

• addMarker

  protected void addMarker(Marker marker, boolean unique)

  Add a marker to the collection

• addSequences

  protected void addSequences(String chr, String chrSeq)

  Add genomic reference sequences

• adjustChromosomes

  protected void adjustChromosomes()

  Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)

• adjustTranscripts

  protected void adjustTranscripts()

  Adjust transcripts: recalculate start, end, strand, etc.

• beforeExonSequences

  protected void beforeExonSequences()

  Perform some actions before reading sequences

• codingFromCds

  protected void codingFromCds()

  Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf | cut -f 2 | ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding

• collapseZeroLenIntrons

  protected void collapseZeroLenIntrons()

  Collapse exons having zero size introns between them

• create

  public abstract SnpEffectPredictor create()

• createRandSequences

  protected void createRandSequences()

  Create random sequences for exons Note: This is only used for test cases!

• deleteRedundant

  protected void deleteRedundant()

  Consolidate transcripts: If two exons are one right next to the other, join them E.g. exon1:1234-2345, exon2:2346-2400 => exon:1234-2400 This happens mostly in GTF files, where the stop-codon is specified separated from the exon info.

• exonsFromCds

  protected void exonsFromCds()

  Create exons from CDS info

• exonsFromCds

  protected void exonsFromCds(Transcript tr)

  Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process

  Parameters:

  tr - : Transcript with CDS info, but no exons

• findGene

  protected Gene findGene(String id)

• findGene

  protected Gene findGene(String geneId, String id)

• findMarker

  protected Marker findMarker(String id)

• findTranscript

  protected Transcript findTranscript(String id)

• findTranscript

  protected Transcript findTranscript(String trId, String id)

• getOrCreateChromosome

  protected Chromosome getOrCreateChromosome(String chromoName)

  Get a chromosome. If it doesn't exist, create it

• getProteinByTrId

  public Map<String,String> getProteinByTrId()

• parsePosition

  protected int parsePosition(String posStr)

  Parse a string as a 'position'. Note: It subtracts 'inOffset' so that all coordinates are zero-based

• readExonSequences

  protected void readExonSequences()

  Read exon sequences from a FASTA file

• replaceTranscript

  protected void replaceTranscript(Transcript trOld, Transcript trNew)

• setCircularCorrectLargeGap

  public void setCircularCorrectLargeGap(boolean circularCorrectLargeGap)

• setCreateRandSequences

  public void setCreateRandSequences(boolean createRandSequences)

• setDebug

  public void setDebug(boolean debug)

• setFastaFile

  public void setFastaFile(String fastaFile)

• setFileName

  public void setFileName(String fileName)

• setRandom

  public void setRandom(Random random)

• setReadSequences

  public void setReadSequences(boolean readSequences)

  Read sequences? Note: This is only used for debugging and testing

• setStoreSequences

  public void setStoreSequences(boolean storeSequences)

• setVerbose

  public void setVerbose(boolean verbose)

• showChromoNamesDifferences

  protected String showChromoNamesDifferences()

  Shw differences in chromosome names