5ba0549a475bafee7d17a3fa9fc3a42d08cb1c11
tdreszer
  Fri May 3 17:06:11 2013 -0700
Clarified some comments based upon Angie's feedback.  Thanks.
diff --git src/lib/vcfBits.c src/lib/vcfBits.c
index 0ed67b9..d0c5da6 100644
--- src/lib/vcfBits.c
+++ src/lib/vcfBits.c
@@ -212,49 +212,49 @@
 
 struct vcfRecord *record = records ? records : vcff->records;
 for (;record != NULL; record = record->next)
     {
     struct variantBits *vBits = vcfOneRecordToVariantBits(vcff, record, phasedOnly, homozygousOnly);
     if (unphasedBits)
         vBits->unphased = vcfRecordUnphasedBits(vcff, record);
     slAddHead(&vBitsList,vBits);
     }
 slReverse(&vBitsList);
 
 return vBitsList;
 }
 
 int vcfVariantBitsDropSparse(struct variantBits **vBitsList, int haploGenomeMin,
-                             boolean dropRefErrors)
+                             boolean dropRefMissing)
 // Drops vBits found in less than a minimum number of haplotype genomes.  Supplying 1 will
-// drop variants found in no haplotype genomes.  Declaring dropRefErrors will drop variants
-// in all haplotype genomes (variants where reference is wrong).
-// Returns count of vBits structure that were dropped.
+// drop variants found in no haplotype genomes.  Declaring dropRefMissing will drop variants
+// in all haplotype genomes (variants where reference is not represented in dataset and
+// *might* be in error). Returns count of vBits structure that were dropped.
 {
 struct variantBits *vBitsKeep = NULL;
 struct variantBits *vBits = NULL;
 int dropped = 0;
 while ((vBits = slPopHead(vBitsList)) != NULL)
     {
     if (vBits->bitsOn >= haploGenomeMin)
         slAddHead(&vBitsKeep,vBits);
     else
         dropped++;  // if not demoted, drop memory, since this is on lm
     }
 *vBitsList = vBitsKeep;
 
-if (dropRefErrors)
+if (dropRefMissing)
     {
     vBitsKeep = NULL;
     while ((vBits = slPopHead(vBitsList)) != NULL)
         {
         boolean foundRef = FALSE;
         int genoIx = 0;
         for (; !foundRef && genoIx < vBits->genotypeSlots; genoIx++)
             {
             int haploIx = 0;
             for (; !foundRef && haploIx < vBits->haplotypeSlots; haploIx++)
                 {
                 if (bitCountRange(vBits->bits,
                                   vBitsSlot(vBits,genoIx,haploIx,0), vBits->alleleSlots) == 0)
                     foundRef = TRUE;
                 }