70d4208efa11f262ba5591198214c9ccdc6b54ae
angie
  Mon Aug 22 22:24:05 2011 -0700
Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code.  Tested all fields,
selected fields, bed output; filter, intersection, schema
on 3 flavors of vcfTabix:
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz
ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz

diff --git src/inc/vcf.h src/inc/vcf.h
index 2cd150a..f63a309 100644
--- src/inc/vcf.h
+++ src/inc/vcf.h
@@ -76,31 +76,31 @@
     char **filters;		// Code(s) described in header for failed filters (or PASS or .)
     int infoCount;		// Number of components of INFO column
     struct vcfInfoElement *infoElements;	// Array of INFO column components
     char *format;		// Optional column containing ordered list of genotype components
     char **genotypeUnparsedStrings;	// Temporary array of unparsed optional genotype columns
     struct vcfGenotype *genotypes;	// If built, array of parsed genotype components;
 					// call vcfParseGenotypes(record) to build.
     struct vcfFile *file;	// Pointer back to parent vcfFile
 };
 
 struct vcfFile
 /* Info extracted from a VCF file.  Manages all memory for contents.
  * Clearly borrowing structure from MarkD's gff3File. :) */
 {
     char *fileOrUrl;		// VCF local file path or URL
-    struct hash *metaDataHash;	// Store all header metadata lines here
+    char *headerString;		// Complete original header including newlines.
     int majorVersion;		// 4 etc.
     int minorVersion;		// 0, 1 etc.
     struct vcfInfoDef *infoDefs;	// Header's definitions of INFO column components
     struct vcfInfoDef *filterDefs;	// Header's definitions of FILTER column failure codes
     struct vcfInfoDef *altDefs;	// Header's defs of symbolic alternate alleles (e.g. DEL, INS)
     struct vcfInfoDef *gtFormatDefs;	// Header's defs of GENOTYPE compnts. listed in FORMAT col.
     int genotypeCount;		// Number of optional genotype columns described in header
     char **genotypeIds;		// Array of optional genotype column names described in header
     struct vcfRecord *records;	// VCF data rows, sorted by position
     struct hash *byName;		// Hash records by name -- not populated until needed.
     struct hash *pool;		// Used to allocate string values that tend to
 				// be repeated in the files.  hash's localMem is also 
 				// use to allocated memory for all other objects.
     struct lineFile *lf;	// Used only during parsing
     int maxErr;			// Maximum number of errors before aborting