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/README src/hg/utils/pslMap/README
deleted file mode 100644
index abeab26..0000000
--- src/hg/utils/pslMap/README
+++ /dev/null
@@ -1,64 +0,0 @@
-
-Overview:
-
-pslMap is an alignment tool than combines two alignment, sharing a common
-sequence, to produce another alignment.  This is an implementation of the
-TransMap alignment algorithm on PSL files.
-
-Given alignments of
-      a to b
-      b to c
-it produces an alignment of a to c by projecting through b.  This differs from
-liftOver in that it does a base-by-base mapping, which may insert or delete
-bases within a block.  The mappings produced by lifeOver are block-level,
-which may expand or contract the size of blocks.
-
-Description:
-
-   pslMap [options] inPsl mapFile outPsl
-
-The pslMap program takes alignments the PSL format alignment in the inPsl file
-and projects the alignments through the overlapping mapFile alignments, which
-can be in PSL or chain format.  The resulting alignments are written to outPsl
-file in PSL format.
-
-The target side of inPsl must be the same set of sequences as the query side
-of mapFile.  Input alignments with target sequence names that don't match any
-mapping file query sequence names are discarded.  If the matching target and
-query name have different sequence sizes, an error will be generated.  The
-options -swapMap and -swapIn can be used to swap the query and target sides of
-either alignment if the are not in the required orientation.
-
-Special handling is provide to support mapping proteins to a genome.  If the
-input PSL is a protein to DNA PSL, the protein coordinates will be converted
-to CDS coordinates in the output PSL.  That is, each coordinate in the protein
-will be multiplied by three.  This is used when mapping proteins to the genome
-by mapping protein to mRNA alignments with mRNA to genome alignments.  Unlike
-most protein to genome alignment process, the resulting CDS to genome
-alignment is able to represent amino acids that are coded for by spliced
-codons.
-
-
-Examples:
-
-Mapping cDNAs between organism using syntenic chains of genomic alignments:
-
-   # map a PSL file of mouse cDNA to genomic (mm8) alignments to hg18 in
-   # mmCDna.mm8.psl
-
-   # chains are mm8 query to hg18 target
-   chainDir=/cluster/data/hg18/bed/blastz.mm8/axtChain
-
-   # create a subset of syntenic chains for 
-   netFilter -syn $chainDir/hg18.mm8.net.gz >hg18.mm8.syn.net
-   netChainSubset -wholeChains hg18.mm8.syn.net $chainDir/hg18.mm8.all.chain.gz hg18.mm8.syn.chain
-
-   pslMap -chainMapFile mmCDna.mm8.psl hg18.mm8.syn.chain mmCDna.hg18.psl
-
-   # depending on desired results, pslCDnaFilter can be used to filter results
-
-Citation:
-  Jingchun Zhu, J. Zachary Sanborn, Mark Diekhans, Craig B. Lowe, Tom H. Pringle, and David Haussler.
-  Comparative genomics search for losses of long-established genes on the human lineage.
-  PLoS Computational Biology, 3:e247 EP , Dec 2007.
-  http://dx.doi.org/10.1371/journal.pcbi.0030247