e315c976feed717d2cdd38a1c5e4e51d53e9a3fb
hartera
  Fri Apr 19 15:56:46 2013 -0700
Removed column no longer used that was commented out. Modified description for alignGapCount field.
diff --git src/hg/inc/ucscRetroInfo.h src/hg/inc/ucscRetroInfo.h
index 5d2aa67..476c31a 100644
--- src/hg/inc/ucscRetroInfo.h
+++ src/hg/inc/ucscRetroInfo.h
@@ -33,32 +33,31 @@
     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 alignGapCount;	/* old simple intron count col34 */
+    int alignGapCount;	/* 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 */