0ede364a2dcb452681933d5a3579b4f05d90a245
markd
  Sun Jul 5 15:16:27 2020 -0700
fixed bug where totalSeqSize was not stored in index, now hgBlat works

diff --git src/inc/genoFind.h src/inc/genoFind.h
index bdf59e8..fd2209d 100644
--- src/inc/genoFind.h
+++ src/inc/genoFind.h
@@ -93,61 +93,62 @@
     {
     int maxPat;                          /* Max # of times pattern can occur
                                           * before it is ignored. */
     int minMatch;                        /* Minimum number of tile hits needed
                                           * to trigger a clump hit. */
     int maxGap;                          /* Max gap between tiles in a clump. */
     int tileSize;			 /* Size of each N-mer. */
     int stepSize;			 /* Spacing between N-mers. */
     int tileSpaceSize;                   /* Number of N-mer values. */
     int tileMask;			 /* 1-s for each N-mer. */
     int sourceCount;			 /* Count of source files. */
     bool isPep;			 	 /* Is a peptide. */
     bool allowOneMismatch;		 /* Allow a single mismatch? */
     bool noSimpRepMask;			  /* Dis-Allow simple repeat masking. */
     int segSize;			 /* Index is segmented if non-zero. */
-    struct gfSeqSource *sources;         /* List of sequence sources. */
     bits32 totalSeqSize;		 /* Total size of all sequences. */
+    struct gfSeqSource *sources;         /* List of sequence sources. */
     bits32 *listSizes;                   /* Size of list for each N-mer */
     void *allocated;                     /* Storage space for all lists. */
     bits32 **lists;                      /* A list for each N-mer. Used if
                                           * isSegmented is false. */
     bits16 **endLists;                   /* A more complex list for each N-mer.
                                           * Used if isSegmented is true.
 					  * Values come in groups of threes.
 					  * The first is the packed last few
 					  * letters of the tile.  The next two
 					  * are the offset in the genome.  This
 					  * would be a struct but that would take
 					  * 8 bytes instead of 6, or nearly an
 					  * extra gigabyte of RAM. */
     };
 
 
 void genoFindFree(struct genoFind **pGenoFind);
 /* Free up a genoFind index. */
 
 struct gfSeqSource *gfFindNamedSource(struct genoFind *gf, char *name);
 /* Find target of given name.  Return NULL if none. */
 
 struct genoFindIndex
 /* container for genoFind indexes, sorting either an untranslated index on six translated indexes.
  * these can be created in memory or saved to a file to quickly mmap */
 {
     void *memMapped;     /* memory mapped if non-NULL, with amount allocated */
     size_t memLength;
     bool isTrans;        /* is this translated? */
+    bool noSimpRepMask;  /* Suppresses simple repeat masking for very small genomes */
     struct genoFind *untransGf;
     struct genoFind *transGf[2][3];
 };
 
 struct genoFindIndex* genoFindIndexBuild(int fileCount, char *seqFiles[],
                                          int minMatch, int maxGap, int tileSize,
                                          int repMatch, boolean doTrans, char *oocFile,
                                          boolean allowOneMismatch, boolean doMask,
                                          int stepSize, boolean noSimpRepMask);
 /* build a untranslated or translated index */
 
 void genoFindIndexWrite(struct genoFindIndex *gfIdx, char *fileName);
 /* write index to file that can be mapped */
 
 struct genoFindIndex* genoFindIndexLoad(char *fileName, boolean isTrans);