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/pslSwap/pslSwap.c src/hg/pslSwap/pslSwap.c
deleted file mode 100644
index a759376..0000000
--- src/hg/pslSwap/pslSwap.c
+++ /dev/null
@@ -1,57 +0,0 @@
-/* pslSwap - reverse target and query in psls */
-
-#include "common.h"
-#include "linefile.h"
-#include "dnautil.h"
-#include "options.h"
-#include "psl.h"
-
-/* command line options */
-static struct optionSpec optionSpecs[] = {
-    {"noRc", OPTION_BOOLEAN},
-    {NULL, 0}
-};
-boolean gNoRc = FALSE;
-
-void usage()
-/* usage message and abort */
-{
-errAbort("pslSwap - swap target and query in psls\n"
-         "usage:\n"
-         "    pslSwap [options] inPsl outPsl\n"
-         "\n"
-         "Options:\n"
-         "  -noRc - don't reverse complement untranslated alignments to\n"
-         "   keep target positive strand.  This will make the target strand\n"
-         "   explict.\n");
-}
-
-void pslSwapFile(char *inPslFile, char *outPslFile)
-/* reverse target and query in a psl file */
-{
-struct lineFile *inLf = pslFileOpen(inPslFile);
-FILE *outFh = mustOpen(outPslFile, "w");
-struct psl *psl;
-
-while ((psl = pslNext(inLf)) != NULL)
-    {
-    pslSwap(psl, gNoRc);
-    pslTabOut(psl, outFh);
-    pslFree(&psl);
-    }
-
-carefulClose(&outFh);
-lineFileClose(&inLf);
-}
-
-int main(int argc, char** argv)
-/* entry */
-{
-optionInit(&argc, argv, optionSpecs);
-if (argc != 3)
-    usage();
-gNoRc = optionExists("noRc");
-dnaUtilOpen();
-pslSwapFile(argv[1], argv[2]);
-return 0;
-}