13db5365510728c1e96d96110a6fe86065949b8a
chmalee
  Thu Sep 24 16:17:54 2020 -0700
Make vcfToBed way more basic  and don't do any special parsing of VCF specific stuff, just chop out requested fields, refs #25010

diff --git src/lib/vcf.c src/lib/vcf.c
index b9df010..ecd5044 100644
--- src/lib/vcf.c
+++ src/lib/vcf.c
@@ -755,31 +755,31 @@
 int wordCount;
 if ((wordCount = lineFileChopTab(vcff->lf, words)) <= 0)
     return NULL;
 wordCount = checkWordCount(vcff, words, wordCount);
 return vcfRecordFromRow(vcff, words);
 }
 
 static boolean noAltAllele(char **alleles, int alleleCount)
 /* Return true if there is no alternate allele (missing value ".") or the given alternate allele
  * is the same as the reference allele. */
 {
 return (alleleCount == 2 &&
         (sameString(alleles[0], alleles[1]) || sameString(".", alleles[1])));
 }
 
-static boolean allelesHavePaddingBase(char **alleles, int alleleCount)
+boolean allelesHavePaddingBase(char **alleles, int alleleCount)
 /* Examine alleles to see if they either a) all start with the same base or
  * b) include a symbolic or 0-length allele.  In either of those cases, there
  * must be an initial padding base that we'll need to trim from non-symbolic
  * alleles. */
 {
 if (sameString(alleles[0], "-"))
     return FALSE;
 else if (noAltAllele(alleles, alleleCount))
     // Don't trim assertion of no change (ref == alt)
     return FALSE;
 boolean hasPaddingBase = TRUE;
 char firstBase = '\0';
 if (isAllNt(alleles[0], strlen(alleles[0])))
     firstBase = alleles[0][0];
 int i;