src/hg/pslMap/usage.txt 1.4

Index: src/hg/pslMap/usage.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslMap/usage.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/pslMap/usage.txt	27 Jul 2007 05:41:48 -0000	1.3
+++ src/hg/pslMap/usage.txt	10 Jul 2009 18:11:56 -0000	1.4
@@ -46,8 +46,12 @@
        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
+  -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 `.'.