060ada2535fca719656219c1214a3e1c16490693
tdreszer
  Wed Nov 9 16:06:41 2011 -0800
Moved as code in hgTables down to lib and access it from hgc and hgTrackUi.  This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
diff --git src/inc/vcf.h src/inc/vcf.h
index f63a309..40d02b8 100644
--- src/inc/vcf.h
+++ src/inc/vcf.h
@@ -1,26 +1,27 @@
 /* VCF: Variant Call Format, version 4.0 / 4.1
  * http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40
  * http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
  * The vcfFile object borrows many memory handling and error reporting tricks from MarkD's
  * gff3File; any local deficiencies are not to reflect poorly on Mark's fine work! :) */
 
 #ifndef vcf_h
 #define vcf_h
 
 #include "hash.h"
 #include "linefile.h"
+#include "asParse.h"
 
 enum vcfInfoType
 /* VCF header defines INFO column components; each component has one of these types: */
     {
     vcfInfoNoType,	// uninitialized value (0) or unrecognized type name
     vcfInfoInteger,
     vcfInfoFloat,
     vcfInfoFlag,
     vcfInfoCharacter,
     vcfInfoString,
     };
 
 union vcfDatum
 /* Container for a value whose type is specified by an enum vcfInfoType. */
     {
@@ -203,16 +204,19 @@
 struct vcfInfoDef *vcfInfoDefForKey(struct vcfFile *vcff, const char *key);
 /* Return infoDef for key, or NULL if it wasn't specified in the header or VCF spec. */
 
 void vcfParseGenotypes(struct vcfRecord *record);
 /* Translate record->genotypesUnparsedStrings[] into proper struct vcfGenotype[].
  * This destroys genotypesUnparsedStrings. */
 
 const struct vcfGenotype *vcfRecordFindGenotype(struct vcfRecord *record, char *sampleId);
 /* Find the genotype and associated info for the individual, or return NULL.
  * This calls vcfParseGenotypes if it has not already been called. */
 
 struct vcfInfoDef *vcfInfoDefForGtKey(struct vcfFile *vcff, const char *key);
 /* Look up the type of genotype FORMAT component key, in the definitions from the header,
  * and failing that, from the keys reserved in the spec. */
 
+struct asObject *vcfAsObj();
+// Return asObject describing fields of VCF
+
 #endif // vcf_h