ca9aa98fe525e6a571de9edb55def7cad009c920
markd
  Fri Jun 30 00:20:40 2023 -0700
add pslMap -check option to check for valid PSLs to aid in debugging

diff --git src/utils/pslMap/usage.txt src/utils/pslMap/usage.txt
index f5075e4..c1cea4a 100644
--- src/utils/pslMap/usage.txt
+++ src/utils/pslMap/usage.txt
@@ -19,30 +19,32 @@
 valid, along with the type of output,
 
      inPslType   mapPslType  outPslType
      na_na       na_na       na_na
      prot_prot   prot_prot   prot_prot
      prot_na     na_na       cds_na
      prot_prot   na_na       cds_na
      prot_prot   prot_na     cds_na
 
 A chain file may be used instead mapPsl.
 
 Options:
   -chainMapFile - mapFile is a chain file instead of a psl file
   -swapMap - swap query and target sides of map file.
   -swapIn - swap query and target sides of inPsl file.
+  -check - validate input, mapping, and mapped PSLs.  This does slow
+   down the program some, so it is optional.
   -suffix=str - append str to the query ids in the output
    alignment.  Useful with protein alignments, where the result
    is not actually and alignment of the protein.
   -keepTranslated - if either psl is translated, the output psl
    will be translated (both strands explicted).  Normally an
    untranslated psl will always be created
   -mapFileWithInQName - The first column of the mapFile PSL records are a qName,
    the remainder is a standard PSL.  When an inPsl record is mapped, only
    mapping records are used with the corresponding qName.
   -inType=type - input alignment type (prot-port, prot-na, na-na)
    This is the type after swapping if -swapIn is supplied.
   -mapType=type - map alignment type (prot-port, prot-na, na-na)
    This is the type after swapping if -swapMap is supplied.
   -mapInfo=file - output a file with information about each mapping.
    The file has the following columns: