dab0887917cbe0472fdc7505b388c455b5adbb53
hartera
  Tue Mar 24 14:12:05 2015 -0700
Updated column descriptions.

diff --git src/hg/lib/ucscRetroInfo.as src/hg/lib/ucscRetroInfo.as
index 016a073..a0f0257 100644
--- src/hg/lib/ucscRetroInfo.as
+++ src/hg/lib/ucscRetroInfo.as
@@ -4,39 +4,39 @@
     string chrom;	"Reference sequence chromosome or scaffold col1"
     uint chromStart;	"pseudogene alignment start position col2"
     uint chromEnd;      "pseudogene alignment end position col3"
     string name;        "Name of pseudogene col4"
     uint score;         "score of pseudogene with gene col5"
     char[2] strand;     "+ or -"
     uint thickStart;    "Start of where display should be thick (start codon)"
     uint thickEnd;      "End of where display should be thick (stop codon)"
     uint reserved;      "Always zero for now"
     int blockCount;     "Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts; "Start positions relative to chromStart"
     int retroExonCount;	"number of exons in retroGene col13"
     int axtScore;       "blastz score, parent mrna aligned to pseudogene col14"
     string type;	"type of evidence col15"
-    string gChrom;	"Chromosome name col16"
-    int gStart;	        "gene alignment start position col17"
-    int gEnd;           "gene alignment end position col18"
-    char[2] gStrand;    "strand of gene col19"
+    string gChrom;	"chromosome name for parent gene col16"
+    int gStart;	        "parent gene alignment start position col17"
+    int gEnd;           "parent gene alignment end position col18"
+    char[2] gStrand;    "strand of parent gene col19"
     uint parentSpliceCount;     "# of splice sites in parent gene col20"
     uint geneOverlap;   "bases overlapping col21"
     uint 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"
+    int exonCover;      "number of exons in parent gene covered col24"
     uint intronCount;   "number of introns in pseudogene col25"
     uint bestAliCount;  "number of good mrnas aligning col26"
     uint matches;       "matches + repMatches col27"
     uint qSize;         "aligning bases in pseudogene col28"
     uint qEnd;          "end of cdna alignment col29"
     uint tReps;         "repeats in gene col30"
     uint coverage;      "% of bases that align to gene col31"
     int label;          "1=pseudogene,-1 not pseudogene -2 expressed retroGene col32"
     uint milliBad;      "milliBad score, pseudogene aligned to genome col33"
     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"
     string refSeq;	"Name of closest regSeq to gene col38"
     int rStart;	        "refSeq alignment start position col39"