3cf1c19c268c97a7c21bffb98fae92c051405773
braney
  Mon Mar 23 07:25:05 2015 -0700
changing the format of bigPsl around a little

diff --git src/hg/lib/bigPsl.as src/hg/lib/bigPsl.as
index 16df4e5..d805c07 100644
--- src/hg/lib/bigPsl.as
+++ src/hg/lib/bigPsl.as
@@ -1,34 +1,29 @@
 table bigPsl
 "bigPsl pairwise alignment"
    (
    string chrom;       "Reference sequence chromosome or scaffold"
    uint   chromStart;  "Start position in chromosome"
    uint   chromEnd;    "End position in chromosome"
    string name;        "Name or ID of item, ideally both human readable and unique"
    uint score;         "Score (0-1000)"
    char[1] strand;     "+ or - for strand"
    uint thickStart;    "Start of where display should be thick (start codon)"
    uint thickEnd;      "End of where display should be thick (stop codon)"
    uint reserved;       "RGB value (use R,G,B string in input file)"
    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."
-   uint matches;       "Number of matching bases that aren't repeats."
-   uint misMatches;    "Number of bases that don't match."
-   uint repMatches;    "Number of matching bases that are part of repeats."
-   uint nCount;        "Number of 'N' bases."
-   uint qNumInsert;    "Number of inserts in query."
-   uint qBaseInsert;   "Number of bases inserted into query."
-   uint tNumInsert;    "Number of inserts in target."
-   uint tBaseInsert;   "Number of bases inserted into target."
    )