
pslMap is a tool for projecting alignments to another sequence through a
common alignment.  This is an implementation of the TransMap algorithm:
Given alignments of
      a -> b
      b -> c
it produces an alignment of a -> c.

Examples:

Mapping cDNAs between organism using syntenic chains of genomic alignments:

   # to map a psl of mouse cDNA to genomoic (mm8) alignments to hg18
   # in mmCDna.mm8.psl

   chainDir=/cluster/data/mm8/bed/blastz.hg18/axtChain

   netFilter -syn $chainDir/mm8.hg18.net.gz >mm8.hg18.syn.net
   netChainSubset -wholeChains mm8.hg18.syn.net $chainDir/mm8.hg18.all.chain.gz mm8.hg18.syn.chain

   # since target of chains is mm8, we must use -swapMap option
          
   pslMap -chainMapFile -swapMap mmCDna.mm8.psl hg18.syn.chain mmCDna.hg18.psl
