text: /* annoFormatVep -- write functional predictions in the same format as Ensembl's
   * Variant Effect Predictor to fileName, interpreting input rows according to config.
   * See http://uswest.ensembl.org/info/docs/variation/vep/vep_formats.html */
  
  /* Copyright (C) 2013 The Regents of the University of California 
   * See README in this or parent directory for licensing information. */
  
  #ifndef ANNOFORMATVEP_H
  #define ANNOFORMATVEP_H
  
  #include "annoFormatter.h"
  
  struct annoFormatter *annoFormatVepNew(char *fileName, boolean doHtml,
  				       struct annoStreamer *variantSource,
  				       char *variantDescription,
  				       struct annoStreamer *gpVarSource,
  				       char *gpVarDescription,
  				       struct annoStreamer *snpSource,
  				       char *snpDescription,
  				       struct annoAssembly *assembly);
  /* Return a formatter that will write functional predictions in the same format as Ensembl's
   * Variant Effect Predictor to fileName (can be "stdout").
   * variantSource and gpVarSource must be provided; snpSource can be NULL. */
  
  void annoFormatVepAddExtraItem(struct annoFormatter *fSelf, struct annoStreamer *extraSource,
  			       char *tag, char *description, char *column, boolean isBoolean);
  /* Tell annoFormatVep that it should include the given column of extraSource
   * in the EXTRAS column with tag.  The VEP header will include tag's description.
   * For some special-cased sources e.g. dbNsfp files, column may be NULL/ignored.
   * If isBoolean, the column's description won't be output, only whether a match was found. */
  
  void annoFormatVepAddRegulatory(struct annoFormatter *self, struct annoStreamer *regSource,
  				char *tag, char *description, char *column);
  /* Tell annoFormatVep to use the regulatory_region_variant consequence if there is overlap
   * with regSource, and to include the given column of regSource in the EXTRAS column.
   * The VEP header will include tag's description. */
  
  void annoFormatVepSetHgvsOutOptions(struct annoFormatter *fSelf, uint hgvsOutOptions);
  /* Import the HGVS output options described in hgHgvs.h */
  
  #endif//ndef ANNOFORMATVEP_H
  