b95ff3835509b242bd9007ba55c4f60c1022da47
markd
  Thu Dec 30 14:58:16 2010 -0800
moved to programs to hg/utils, fixed build of distributed utilities
diff --git src/hg/pslMap/usage.txt src/hg/pslMap/usage.txt
deleted file mode 100644
index 46b11b2..0000000
--- src/hg/pslMap/usage.txt
+++ /dev/null
@@ -1,57 +0,0 @@
-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
-  -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 `.'.