02336754147822f5aa61ba13277123b2cc629001
markd
  Thu May 20 08:38:55 2021 -0700
Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies.

diff --git src/hg/utils/pslMap/usage.txt src/hg/utils/pslMap/usage.txt
deleted file mode 100644
index 84c4224..0000000
--- src/hg/utils/pslMap/usage.txt
+++ /dev/null
@@ -1,64 +0,0 @@
-pslMap - map PSLs alignments to new targets using alignments of the old target to the new target.
-usage:
-   pslMap [options] inPsl mapFile outPsl
-
-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 all the targets 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.
-
-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
-  -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.
-  -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 `.'.
-  -verbose=n  - verbose output
-     2 - show each overlap and the mapping