acca3deffc05c4d8d11590a1cf3d893763254712
angie
  Thu Oct 31 13:43:05 2019 -0700
dbSnp153: Adding new ucscNotes suggested by Ana Benet: clinvar{Benign,Conflicting,Pathogenic}, rareAll, rareSome.  refs #23283

diff --git src/hg/inc/bigDbSnp.h src/hg/inc/bigDbSnp.h
index 6a82ec5..dcfd84f 100644
--- src/hg/inc/bigDbSnp.h
+++ src/hg/inc/bigDbSnp.h
@@ -1,117 +1,122 @@
 /* bigDbSnp.h was originally generated by the autoSql program, which also 
  * generated bigDbSnp.c and bigDbSnp.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef BIGDBSNP_H
 #define BIGDBSNP_H
 
 #define BIGDBSNP_NUM_COLS 17
 
 extern char *bigDbSnpCommaSepFieldNames;
 
 enum bigDbSnpClass
     {
     bigDbSnpSnv = 0,
     bigDbSnpMnv = 1,
     bigDbSnpIns = 2,
     bigDbSnpDel = 3,
     bigDbSnpDelins = 4,
     bigDbSnpIdentity = 5,
     };
 struct bigDbSnp
 /* Variant summary data extracted from dbSNP, 2019 and later */
     {
     struct bigDbSnp *next;  /* Next in singly linked list. */
     char *chrom;	/* Reference sequence chromosome or scaffold */
     unsigned chromStart;	/* Start position in chrom */
     unsigned chromEnd;	/* End position in chrom */
     char *name;	/* dbSNP Reference SNP (rs) identifier */
     char *ref;	/* Reference allele; usually major allele, but may be minor allele */
     int altCount;	/* Number of alternate alleles (usually 1) */
     char **alts;	/* Alternate (non-reference) alleles; may include major allele */
     unsigned shiftBases;	/* Bases by which an indel placement could be shifted left or right (display shows thin line over uncertain region, shifts minimal representation right) */
     int freqSourceCount;	/* Number of projects reporting frequencies in current dbSNP build */
     double *minorAlleleFreq;	/* Minor allele frequency, i.e. second highest allele frequency, from each frequency source; NaN if no data from project */
     char **majorAllele;	/* Allele most frequently observed by each source */
     char **minorAllele;	/* Allele second most frequently observed by each source */
     unsigned maxFuncImpact;	/* Sequence Ontology (SO) ID number for greatest functional impact on gene; 0 if no SO terms are annotated */
     enum bigDbSnpClass class;	/* Variation class/type */
     char *ucscNotes;	/* Interesting or anomalous properties noted by UCSC */
     long long _dataOffset;	/* Offset into bigDbSnpDetails file for line with more info */
     int _dataLen;	/* Length of line in bigDbSnpDetails */
     };
 
 struct bigDbSnp *bigDbSnpLoad(char **row);
 /* Load a bigDbSnp from row fetched with select * from bigDbSnp
  * from database.  Dispose of this with bigDbSnpFree(). */
 
 struct bigDbSnp *bigDbSnpLoadAll(char *fileName);
 /* Load all bigDbSnp from whitespace-separated file.
  * Dispose of this with bigDbSnpFreeList(). */
 
 struct bigDbSnp *bigDbSnpLoadAllByChar(char *fileName, char chopper);
 /* Load all bigDbSnp from chopper separated file.
  * Dispose of this with bigDbSnpFreeList(). */
 
 #define bigDbSnpLoadAllByTab(a) bigDbSnpLoadAllByChar(a, '\t');
 /* Load all bigDbSnp from tab separated file.
  * Dispose of this with bigDbSnpFreeList(). */
 
 struct bigDbSnp *bigDbSnpCommaIn(char **pS, struct bigDbSnp *ret);
 /* Create a bigDbSnp out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bigDbSnp */
 
 void bigDbSnpFree(struct bigDbSnp **pEl);
 /* Free a single dynamically allocated bigDbSnp such as created
  * with bigDbSnpLoad(). */
 
 void bigDbSnpFreeList(struct bigDbSnp **pList);
 /* Free a list of dynamically allocated bigDbSnp's */
 
 void bigDbSnpOutput(struct bigDbSnp *el, FILE *f, char sep, char lastSep);
 /* Print out bigDbSnp.  Separate fields with sep. Follow last field with lastSep. */
 
 #define bigDbSnpTabOut(el,f) bigDbSnpOutput(el,f,'\t','\n');
 /* Print out bigDbSnp as a line in a tab-separated file. */
 
 #define bigDbSnpCommaOut(el,f) bigDbSnpOutput(el,f,',',',');
 /* Print out bigDbSnp as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 // ucscNotes is a comma-separated list of these values.  Developer: if you add a new one here,
 // then also update the descriptions used by bigDbSnpDescribeUcscNote in bigDbSnp.c.
 #define bdsAltIsAmbiguous "altIsAmbiguous"
 #define bdsClassMismatch "classMismatch"
 #define bdsClinvar "clinvar"
+#define bdsClinvarBenign "clinvarBenign"
+#define bdsClinvarConflicting "clinvarConflicting"
+#define bdsClinvarPathogenic "clinvarPathogenic"
 #define bdsClusterError "clusterError"
 #define bdsCommonAll "commonAll"
 #define bdsCommonSome "commonSome"
 #define bdsDiffMajor "diffMajor"
 #define bdsFreqIsAmbiguous "freqIsAmbiguous"
 #define bdsFreqNotRefAlt "freqNotRefAlt"
 #define bdsMultiMap "multiMap"
 #define bdsOverlapDiffClass "overlapDiffClass"
 #define bdsOverlapSameClass "overlapSameClass"
+#define bdsRareAll "rareAll"
+#define bdsRareSome "rareSome"
 #define bdsRefIsAmbiguous "refIsAmbiguous"
 #define bdsRefIsMinor "refIsMinor"
 #define bdsRefIsRare "refIsRare"
 #define bdsRefIsSingleton "refIsSingleton"
 #define bdsRefMismatch "refMismatch"
 #define bdsRevStrand "revStrand"
 
 char *bigDbSnpDescribeUcscNote(char *ucscNote);
 /* Return a string describing ucscNote, unless it is unrecognized in which case return NULL.
  * Do not free returned value. */
 
 char *bigDbSnpClassToString(enum bigDbSnpClass class);
 /* Return the string version of enum bigDbSnpClass.  Do not free result. */
 
 char *bigDbSnpAbbrevAllele(char *allele, char *buf, size_t bufLen);
 /* If allele can be abbreviated to something shorter than itself that fits in buf,
  * and doesn't end up with a tiny bit of abbreviation followed by a bunch of unabbreviated
  * sequence, then put the abbreviation in buf and return buf; otherwise return allele.
  * If allele is the empty string, returns "-" (in buf). */
 
 #endif /* BIGDBSNP_H */