6f8564256fee3371551bcf6249467bb7ba77ca34
braney
  Wed Apr 8 13:13:53 2015 -0700
add a few more stats to bigPsl record (per Jim)

diff --git src/hg/lib/bigPsl.as src/hg/lib/bigPsl.as
index d805c07..ce8e583 100644
--- src/hg/lib/bigPsl.as
+++ src/hg/lib/bigPsl.as
@@ -13,17 +13,20 @@
     int blockCount;     "Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts; "Start positions relative to chromStart"
 
     string  oChrom;     "Other chromosome in the alignment"
     uint    oChromStart;"Start position in other chromosome"
     uint    oChromEnd;  "End position in other chromosome"
     char[1] oStrand;    "+ or - for other strand"
     uint    oChromSize; "Size of other chromosome."
     int[blockCount] oChromStarts; "Start positions relative to oChromStart"
 
     string  oSequence;  "Sequence on other chrom (or edit list, or empty)"
     uint    oBlock;     "Block number on other sequence"
 
     uint match;        "Number of bases matched."
+    unsigned misMatch; " Number of bases that don't match "
+    unsigned repMatch; " Number of bases that match but are part of repeats "
+    unsigned nCount;   " Number of 'N' bases "
     )