d41531259de6cb8aafd3b0d336518f2e8d6cfb61
markd
  Tue May 26 17:13:04 2020 -0700
Hiram is right, this is useless; what is really needed is for mafOrder to have an option to orient the reference sequence to the positive strand

diff --git src/hg/ratStuff/mafRc/mafRc.c src/hg/ratStuff/mafRc/mafRc.c
deleted file mode 100644
index 02412c8..0000000
--- src/hg/ratStuff/mafRc/mafRc.c
+++ /dev/null
@@ -1,85 +0,0 @@
-/* mafRc - Reverse-complement a MAF. */
-#include "common.h"
-#include "linefile.h"
-#include "options.h"
-#include "jksql.h"
-#include "maf.h"
-
-void usage()
-/* Explain usage and exit. */
-{
-errAbort(
-  "mafRc - Reverse-complement a MAF\n"
-  "usage:\n"
-  "   mafRc inMafName outMafName\n"
-  );
-}
-
-/* Command line validation table. */
-static struct optionSpec options[] = {
-   {NULL, 0},
-};
-
-static void exchangeInts(int *i1, int *i2)
-/* exchange two ints */
-{
-int ihold = *i1;
-*i1 = *i2;
-*i2 = ihold;
-}
-
-static void exchangeChars(char *c1, char *c2)
-/* exchange two chars */
-{
-char chold = *c1;
-*c1 = *c2;
-*c2 = chold;
-}
-
-static void mafRcComponent(struct mafComp *mafComp)
-/* reverse-complement a MAF component */
-{
-mafComp->strand = (mafComp->strand == '+') ? '-' : '+';
-mafComp->start = mafComp->srcSize - mafComp-> start;
-if (mafComp->text != NULL)
-    reverseComplement(mafComp->text, strlen(mafComp->text));
-if (mafComp->quality != NULL)
-    reverseBytes(mafComp->quality, strlen( mafComp->quality));
-exchangeChars(&mafComp->leftStatus, &mafComp->rightStatus);
-exchangeInts(&mafComp-> leftLen, &mafComp->rightLen);
-}
-
-static void mafRcBlock(struct mafAli *mafAli)
-/* reverse-complement a MAF block */
-{
-struct mafComp *mafComp;
-for (mafComp = mafAli->components; mafComp != NULL; mafComp = mafComp->next)
-    mafRcComponent(mafComp);
-}
-
-static void mafRc(char *inMafName, char *outMafName)
-/* mafRc - Reverse-complement a MAF. */
-{
-struct mafFile* inMaf = mafOpen(inMafName);
-FILE* outMafFh = mustOpen(outMafName, "w");
-mafWriteStart(outMafFh, inMaf->scoring);
-
-struct mafAli *mafAli;
-while ((mafAli = mafNext(inMaf)) != NULL)
-    {
-    mafRcBlock(mafAli);
-    mafWrite(outMafFh, mafAli);
-    mafAliFree(&mafAli);
-    }
-carefulClose(&outMafFh);
-}
-
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-optionInit(&argc, argv, options);
-if (argc != 3)
-    usage();
-mafRc(argv[1], argv[2]);
-return 0;
-}