39fb35ef6bc3d14b837e5b6f523acc2f1cedd414
hartera
  Thu Feb 28 10:43:51 2013 -0800
Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount in ucscRetroInfo table so change code and variable names to match.
diff --git src/hg/inc/ucscRetroInfo.h src/hg/inc/ucscRetroInfo.h
index 59d4ae3..5d2aa67 100644
--- src/hg/inc/ucscRetroInfo.h
+++ src/hg/inc/ucscRetroInfo.h
@@ -33,50 +33,50 @@
     char gStrand[3];	/* strand of gene col19 */
     unsigned parentSpliceCount;	/* # of splice sites in parent gene col20 */
     unsigned geneOverlap;	/* bases overlapping col21 */
     unsigned polyA;	/* count of As in polyA col22 */
     int polyAstart;	/* start of polyA, relative to end of pseudogene col23 */
     int exonCover;	/* number of exons in Gene covered col24 */
     unsigned intronCount;	/* number of introns in pseudogene col25 */
     unsigned bestAliCount;	/* number of good mrnas aligning col26 */
     unsigned matches;	/* matches + repMatches col27 */
     unsigned qSize;	/* aligning bases in pseudogene col28 */
     unsigned qEnd;	/* end of cdna alignment col29 */
     unsigned tReps;	/* repeats in gene col30 */
     unsigned coverage;	/* % of bases that align to gene col31 */
     int label;	/* 1=pseudogene,-1 not pseudogene -2 expressed retroGene col32 */
     unsigned milliBad;	/* milliBad score, pseudogene aligned to genome col33 */
-    unsigned oldScore;	/* another heuristic col34 */
-    int oldIntronCount;	/* old simple intron count col35 */
-    int processedIntrons;	/* count of introns removed via retrotransposition col36 */
-    int conservedSpliceSites;	/* conserved splice site count col37 */
-    int maxOverlap;	/* largest overlap with another mrna col38 */
-    char *refSeq;	/* Name of closest regSeq to gene col39 */
-    int rStart;	/* refSeq alignment start position col40 */
-    int rEnd;	/* refSeq alignment end position col41 */
-    char *mgc;	/* Name of closest mgc to gene col42 */
-    int mStart;	/* mgc alignment start position col43 */
-    int mEnd;	/* mgc alignment end position col44 */
-    char *kgName;	/* Name of closest knownGene to gene col45 */
-    int kStart;	/* kg alignment start position col46 */
-    int kEnd;	/* kg alignment end position col47 */
-    char *overName;	/* name of overlapping mrna col48 */
-    int overStart;	/* overlapping mrna start position col49 */
-    int overExonCover;	/* count of overlapping mrna exons col50 */
-    char overStrand[3];	/* strand of overlapping mrna col51 */
-    float posConf;	/* pvalue for positive col52 */
-    unsigned polyAlen;	/* length of polyA col53 */
+/*    unsigned oldScore; */	/* another heuristic col34 */
+    int alignGapCount;	/* old simple intron count col34 */
+    int processedIntrons;	/* count of introns removed via retrotransposition col35 */
+    int conservedSpliceSites;	/* conserved splice site count col36 */
+    int maxOverlap;	/* largest overlap with another mrna col37 */
+    char *refSeq;	/* Name of closest regSeq to gene col38 */
+    int rStart;	/* refSeq alignment start position col39 */
+    int rEnd;	/* refSeq alignment end position col40 */
+    char *mgc;	/* Name of closest mgc to gene col41 */
+    int mStart;	/* mgc alignment start position col42 */
+    int mEnd;	/* mgc alignment end position col43 */
+    char *kgName;	/* Name of closest knownGene to gene col44 */
+    int kStart;	/* kg alignment start position col45 */
+    int kEnd;	/* kg alignment end position col46 */
+    char *overName;	/* name of overlapping mrna col47 */
+    int overStart;	/* overlapping mrna start position col48 */
+    int overExonCover;	/* count of overlapping mrna exons col49 */
+    char overStrand[3];	/* strand of overlapping mrna col50 */
+    float posConf;	/* pvalue for positive col51 */
+    unsigned polyAlen;	/* length of polyA col52 */
     };
 
 struct ucscRetroInfo *ucscRetroInfoLoadByQuery(struct sqlConnection *conn, char *query);
 /* Load all ucscRetroInfo from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with ucscRetroInfoFreeList(). */
 
 void ucscRetroInfoSaveToDb(struct sqlConnection *conn, struct ucscRetroInfo *el, char *tableName, int updateSize);
 /* Save ucscRetroInfo as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Note that strings must be escaped to allow insertion into the database.