18d303bb4f14e1edff401c8a85276ff1344f0f37
angie
Tue Apr 3 10:18:14 2012 -0700
Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row
declaring its type and annoRow{Free,Clone} taking a numCols argument
that is meaningless for wig, now annoRow{Free,Clone} take the row's
source annoStreamer as an argument. The annoStreamer now has public
members (rowType and numCols) that provide all information needed about
the row. annoStreamer constructors need to set rowType.
diff --git src/inc/vcf.h src/inc/vcf.h
index 6394026..6ff5399 100644
--- src/inc/vcf.h
+++ src/inc/vcf.h
@@ -1,226 +1,232 @@
/* 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. */
{
int datInt;
double datFloat;
boolean datFlag;
char datChar;
char *datString;
};
struct vcfInfoDef
/* Definition of INFO column component from VCF header: */
{
struct vcfInfoDef *next;
char *key; // A short identifier, e.g. MQ for mapping quality
int fieldCount; // The number of values to follow the id, or -1 if it varies
enum vcfInfoType type; // The type of values that follow the id
char *description; // Brief description of info
};
struct vcfInfoElement
/* A single INFO column component; each row's INFO column may contain multiple components. */
{
char *key; // An identifier described by a struct vcfInfoDef
int count; // Number of data values following id
union vcfDatum *values; // Array of data values following id
bool *missingData; // Array of flags for missing data values ("." instead of number)
};
struct vcfGenotype
/* A single component of the optional GENOTYPE column. */
{
char *id; // Name of individual/sample (pointer to vcfFile genotypeIds) or .
char hapIxA; // Index of one haplotype's allele: 0=reference, 1=alt, 2=other alt
// *or* if negative, missing data
char hapIxB; // Index of other haplotype's allele, or if negative, missing data
bool isPhased; // True if haplotypes are phased
bool isHaploid; // True if there is only one haplotype (e.g. chrY)
int infoCount; // Number of components named in FORMAT column
struct vcfInfoElement *infoElements; // Array of info components for this genotype call
};
struct vcfRecord
/* A VCF data row (or list of rows). */
{
struct vcfRecord *next;
char *chrom; // Reference assembly sequence name
unsigned int chromStart; // Start offset in chrom
unsigned int chromEnd; // End offset in chrom
char *name; // Variant name from ID column
int alleleCount; // Number of alleles (reference + alternates)
char **alleles; // Alleles: reference first then alternate alleles
char *qual; // . or Phred-scaled score, i.e. -10log_10 P(call in ALT is wrong)
int filterCount; // Number of ;-separated filter codes in FILTER column
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
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
int errCnt; // Error count
};
/* Reserved but optional INFO keys: */
extern const char *vcfInfoAncestralAllele;
extern const char *vcfInfoPerAlleleGtCount; // allele count in genotypes, for each ALT allele,
// in the same order as listed
extern const char *vcfInfoAlleleFrequency; // allele frequency for each ALT allele in the same
// order as listed: use this when estimated from
// primary data, not called genotypes
extern const char *vcfInfoNumAlleles; // total number of alleles in called genotypes
extern const char *vcfInfoBaseQuality; // RMS base quality at this position
extern const char *vcfInfoCigar; // cigar string describing how to align an
// alternate allele to the reference allele
extern const char *vcfInfoIsDbSnp; // dbSNP membership
extern const char *vcfInfoDepth; // combined depth across samples, e.g. DP=154
extern const char *vcfInfoEnd; // end position of the variant described in this
// record (esp. for CNVs)
extern const char *vcfInfoIsHapMap2; // membership in hapmap2
extern const char *vcfInfoIsHapMap3; // membership in hapmap3
extern const char *vcfInfoIs1000Genomes; // membership in 1000 Genomes
extern const char *vcfInfoMappingQuality; // RMS mapping quality, e.g. MQ=52
extern const char *vcfInfoMapQual0Count; // number of MAPQ == 0 reads covering this record
extern const char *vcfInfoNumSamples; // Number of samples with data
extern const char *vcfInfoStrandBias; // strand bias at this position
extern const char *vcfInfoIsSomatic; // indicates that the record is a somatic mutation,
// for cancer genomics
extern const char *vcfInfoIsValidated; // validated by follow-up experiment
/* Reserved but optional per-genotype keys: */
extern const char *vcfGtGenotype; // numeric allele values separated by "/" (unphased)
// or "|" (phased). Allele values are 0 for
// reference allele, 1 for the first allele in ALT,
// 2 for the second allele in ALT and so on.
extern const char *vcfGtDepth; // read depth at this position for this sample
extern const char *vcfGtFilter; // analogous to variant's FILTER field
extern const char *vcfGtLikelihoods; // three floating point log10-scaled likelihoods for
// AA,AB,BB genotypes where A=ref and B=alt;
// not applicable if site is not biallelic.
extern const char *vcfGtPhred; // Phred-scaled genotype likelihoods rounded to closest int
extern const char *vcfGtConditionalQual; // Conditional genotype quality
// i.e. phred quality -10log_10 P(genotype call is wrong,
// conditioned on the site's being variant)
extern const char *vcfGtHaplotypeQualities; // Two phred qualities comma separated
extern const char *vcfGtPhaseSet; // Set of phased genotypes to which this genotype belongs
extern const char *vcfGtPhasingQuality; // Phred-scaled P(alleles ordered wrongly in heterozygote)
extern const char *vcfGtExpectedAltAlleleCount; // Typically used in association analyses
INLINE void vcfPrintDatum(FILE *f, const union vcfDatum datum, const enum vcfInfoType type)
/* Print datum to f in the format determined by type. */
{
switch (type)
{
case vcfInfoInteger:
fprintf(f, "%d", datum.datInt);
break;
case vcfInfoFloat:
fprintf(f, "%f", datum.datFloat);
break;
case vcfInfoFlag:
fprintf(f, "%s", datum.datString); // Flags could have values in older VCF
break;
case vcfInfoCharacter:
fprintf(f, "%c", datum.datChar);
break;
case vcfInfoString:
fprintf(f, "%s", datum.datString);
break;
default:
errAbort("vcfPrintDatum: Unrecognized type %d", type);
break;
}
}
-struct vcfFile *vcfFileMayOpen(char *fileOrUrl, int maxErr, int maxRecords);
-/* Parse a VCF file into a vcfFile object; return NULL if unable.
- * If maxErr not zero, then continue to parse until this number of error have been reached.
- * A maxErr less than zero does not stop and reports all errors.
- * If maxRecords >= 0, then at most that many records will be parsed. */
+struct vcfFile *vcfFileMayOpen(char *fileOrUrl, int maxErr, int maxRecords, boolean parseAll);
+/* Open fileOrUrl and parse VCF header; return NULL if unable.
+ * If parseAll, then read in all lines, parse and store in
+ * vcff->records; if maxErr >= zero, then continue to parse until
+ * there are maxErr+1 errors. A maxErr less than zero does not stop
+ * and reports all errors. */
struct vcfFile *vcfTabixFileMayOpen(char *fileOrUrl, char *chrom, int start, int end,
int maxErr, int maxRecords);
-/* Parse header and rows within the given position range from a VCF file that has been
- * compressed and indexed by tabix into a vcfFile object; return NULL if or if file has
- * no items in range.
- * If maxErr not zero, then continue to parse until this number of error have been reached.
- * A maxErr less than zero does not stop and reports all errors.
- * If maxRecords >= 0, then at most that many records will be parsed. */
+/* Open a VCF file that has been compressed and indexed by tabix and
+ * parse VCF header, or return NULL if unable. If chrom is non-NULL,
+ * seek to the position range and parse all lines in range into
+ * vcff->records. If maxErr >= zero, then continue to parse until
+ * there are maxErr+1 errors. A maxErr less than zero does not stop
+ * and reports all errors. */
+
+struct vcfRecord *vcfRecordFromRow(struct vcfFile *vcff, char **words);
+/* Parse words from a VCF data line into a VCF record structure. */
void vcfFileFree(struct vcfFile **vcffPtr);
/* Free a vcfFile object. */
const struct vcfRecord *vcfFileFindVariant(struct vcfFile *vcff, char *variantId);
/* Return all records with name=variantId, or NULL if not found. */
const struct vcfInfoElement *vcfRecordFindInfo(const struct vcfRecord *record, char *key);
/* Find an INFO element, or NULL. */
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. */
+#define VCF_NUM_COLS 10
+
struct asObject *vcfAsObj();
// Return asObject describing fields of VCF
#endif // vcf_h