pslMap - map PSLs alignments to new targets using alignments of
the old target to the new target.  Given inPsl and mapPsl, where
the target of inPsl is the query of mapPsl, create a new PSL
with the query of inPsl aligned to the target of mapPsl.  If
inPsl is a protein to nucleotide alignment and mapPsl is a
nucleotide to nucleotide alignment, the resulting alignment is
nucleotide to nucleotide alignment of a hypothetical mRNA that
would code for the protein.  This is useful as it gives base
alignments of spliced codons.  A chain file may be used instead
mapPsl

usage:
   pslMap [options] inPsl mapFile outPsl

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.
  -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
  -mapInfo=file - output a file with information about each mapping.
   The file has the following columns:
     o srcQName, srcQStart, srcQEnd, srcQSize - qName, etc of
       psl being mapped (source alignment)
     o srcTName, srcTStart, srcTEnd - tName, etc of psl being
       mapped
     o srcStrand - strand of psl being mapped
     o srcAligned - number of aligned based in psl being mapped
     o mappingQName, mappingQStart, mappingQEnd - qName, etc of
       mapping psl used to map alignment
     o mappingTName, mappingTStart, mappingTEnd - tName, etc of
       mapping psl
     o mappingStrand - strand of mapping psl
     o mappingId - chain id, or psl file row
     o mappedQName mappedQStart, mappedQEnd - qName, etc of
       mapped psl
     o mappedTName, mappedTStart, mappedTEnd - tName, etc of
       mapped psl
     o mappedStrand - strand of mapped psl
     o mappedAligned - number of aligned bases that were mapped
     o qStartTrunc - aligned bases at qStart not mapped due to
       mapping psl/chain not covering the entire soruce psl.
       This is from the start of the query in the positive
       direction.
     o qEndTrunc - similary for qEnd
   If the psl count not be mapped, the mapping* and mapped* columns are empty.
  -mappingPsls=pslFile - write mapping alignments that were used in
   PSL format to this file.  Transformations that were done, such as
   -swapMap, will be reflected in this file.  There will be a one-to-one
   correspondence of rows of this file to rows of the outPsl file.
  -simplifyMappingIds - simplifying mapping ids (inPsl target
   name and mapFile query name) before matching them. This
   first drops everything after the last `-', and then drops
   everything after the last remaining `.'.
