be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/lib/psl.as src/hg/lib/psl.as
new file mode 100644
index 0000000..7114683
--- /dev/null
+++ src/hg/lib/psl.as
@@ -0,0 +1,25 @@
+table psl
+"Summary info about a patSpace alignment"
+    (
+    uint matches;  "Number of bases that match that aren't repeats"
+    uint misMatches; "Number of bases that don't match"
+    uint repMatches; "Number of bases that match but are part of repeats"
+    uint nCount;  "Number of 'N' bases"
+    uint qNumInsert; "Number of inserts in query"
+    int qBaseInsert; "Number of bases inserted in query"
+    uint tNumInsert; "Number of inserts in target"
+    int tBaseInsert; "Number of bases inserted in target"
+    char[2] strand; "+ or - for strand. First character query, second target (optional)"
+    string qName; "Query sequence name"
+    uint qSize; "Query sequence size"
+    uint qStart; "Alignment start position in query"
+    uint qEnd; "Alignment end position in query"
+    string tName; "Target sequence name"
+    uint tSize; "Target sequence size"
+    uint tStart; "Alignment start position in target"
+    uint tEnd; "Alignment end position in target"
+    uint blockCount; "Number of blocks in alignment"
+    uint[blockCount] blockSizes; "Size of each block"
+    uint[blockCount] qStarts; "Start of each block in query."
+    uint[blockCount] tStarts; "Start of each block in target."
+    )