376a3438b1a96761c019bbe128908fc69b5083df
angie
  Thu Jul 30 18:04:05 2020 -0700
Adding VCF_NUM_COLS_BEFORE_GENOTYPES to vcf.h to reduce the proliferation of magic number 9's in the code.

diff --git src/inc/vcf.h src/inc/vcf.h
index 60af930..c9b547f 100644
--- src/inc/vcf.h
+++ src/inc/vcf.h
@@ -328,30 +328,31 @@
  * the ref/ref, ref/alt, alt/alt convention for biallelic variants:
  * 0/0,
  * 0/1, 1/1,
  * 0/2, 1/2, 2/2,
  * 0/3, 1/3, 2/3, 3/3,
  * ... */
 
 void vcfCountGenotypes(struct vcfRecord *rec, int **retGtCounts, int **retAlleleCounts,
                        int *retPhasedCount, int *retDiploidCount);
 /* Tally genotypes and alleles for summary, adding 1 to rec->alleleCount to represent missing data */
 
 char *vcfFilePooledStr(struct vcfFile *vcff, char *str);
 /* Allocate memory for a string from vcff's shared string pool. */
 
 #define VCF_NUM_COLS 10
+#define VCF_NUM_COLS_BEFORE_GENOTYPES 9
 
 struct asObject *vcfAsObj();
 // Return asObject describing fields of VCF
 
 char *vcfGetSlashSepAllelesFromWords(char **words, struct dyString *dy);
 /* Overwrite dy with a /-separated allele string from VCF words,
  * skipping the extra initial base that VCF requires for indel alleles if necessary.
  * Return dy->string for convenience. */
 
 void vcfRecordWriteNoGt(FILE *f, struct vcfRecord *rec);
 /* Write the first 8 columns of VCF rec to f.  Genotype data will be ignored if present. */
 
 // Characters we expect to see in |-separated parts of an ##INFO description that specifies
 // tabular contents:
 #define COL_DESC_WORD_REGEX "[A-Za-z_0-9.-]+"