1c9a4cb6897ec2924b5d7f46e4c6b9162d94d6ba
angie
  Mon Apr 22 16:43:15 2013 -0700
Converted variant and gpFx to use localmem.  Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
and gpFx. refs #6152

diff --git src/hg/inc/variant.h src/hg/inc/variant.h
index 5aa7e70..e90f942 100644
--- src/hg/inc/variant.h
+++ src/hg/inc/variant.h
@@ -1,39 +1,38 @@
 /* variant.h -- a generic variant.  Meant to capture information that's in VCF or pgSNP. */
 
 #ifndef VARIANT_H
 #define VARIANT_H
 
+#include "localmem.h"
 #include "pgSnp.h"
 
 struct allele   // a single allele in a variant. 
     {
     struct allele *next;
     struct variant *variant;
     int length;
     char *sequence;
     };
 
 struct variant   // a single variant
     {
     struct variant *next;  /* Next in singly linked list. */
     char *chrom;	/* Chromosome */
     unsigned chromStart;	/* Start position in chrom */
     unsigned chromEnd;	/* End position in chrom */
     unsigned numAlleles;   /* the number of alleles */
     struct allele *alleles;	/* alleles */
     };
 
 struct variant *variantNew(char *chrom, unsigned start, unsigned end, unsigned numAlleles,
 			   char *slashSepAlleles, struct lm *lm);
 /* Create a variant from basic information that is easy to extract from most other variant
  * formats: coords, allele count, and string of slash-separated alleles. */
 
 struct variant *variantFromPgSnp(struct pgSnp *pgSnp, struct lm *lm);
 /* convert pgSnp record to variant record */
 
-struct allele  *alleleClip(struct allele *allele, int sx, int ex);
-/* clip allele to be inside region defined by sx..ex.  Returns 
- * pointer to new allele which should be freed by alleleFree, or variantFree
- */
+struct allele  *alleleClip(struct allele *allele, int sx, int ex, struct lm *lm);
+/* Return new allele pointing to new variant, both clipped to region defined by sx..ex. */
 
 #endif /* VARIANT_H*/