5711ac6c2bcaeda814ae1049a0661f499775885e
markd
  Wed Dec 13 00:36:12 2023 -0800
change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion

diff --git src/utils/pslProtToRnaCoords/pslProtToRnaCoords.c src/utils/pslProtToRnaCoords/pslProtToRnaCoords.c
index 5f8034c..d3bc6f2 100644
--- src/utils/pslProtToRnaCoords/pslProtToRnaCoords.c
+++ src/utils/pslProtToRnaCoords/pslProtToRnaCoords.c
@@ -1,139 +1,52 @@
 /* pslProtToRnaCoords - Convert protein alignments to RNA coordinates. */
 #include "common.h"
 #include "psl.h"
+#include "pslTransMap.h"
 #include "options.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "pslProtToRnaCoords - Convert protein alignments to RNA coordinates\n"
   "usage:\n"
   "   pslProtToRnaCoords inPsl outPsl\n"
   "\n"
   "Convert either a protein/protein or protein/NA PSL to NA/NA PSL.  This\n"
   "multiplies coordinates and statistics by three.  As this can occasionally\n"
   "results in blocks overlapping, overlap is trimmed as needed.\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
-static void trimOverlapping(bool isProtNaPsl, struct psl *psl, int oBlk)
-/* if this block overlaps the previous block, trim accordingly.  Overlaps
- * can be created with protein to DNA PSLs.  */
-// check for overlap; use int so we can go negative
-{
-int prevQEnd = pslQEnd(psl, oBlk - 1);
-int prevTEnd = pslTEnd(psl, oBlk - 1);
-
-// trim, possibly setting to zero-length
-int overAmt = max((prevQEnd - (int)psl->qStarts[oBlk]), (prevTEnd - (int)psl->tStarts[oBlk]));
-if (overAmt < 0)
-    overAmt = 0;
-else if (overAmt > psl->blockSizes[oBlk])
-    overAmt = psl->blockSizes[oBlk];
-
-psl->qStarts[oBlk] += overAmt;
-psl->tStarts[oBlk] += overAmt;
-psl->blockSizes[oBlk] -= overAmt;
-psl->match -= overAmt;
-}
-
-
-static int updateBlk(bool isProtNaPsl, struct psl *psl, int iBlk, int oBlk)
-/* Update sizes in a block, adjusting start of block if it now
- * overlaps previous block due previous block size expansion.
- * return updated oBlk */
-{
-// update to NA coordinates
-psl->blockSizes[oBlk] = 3 * psl->blockSizes[iBlk];
-psl->qStarts[oBlk] = 3 * psl->qStarts[iBlk];
-if (isProtNaPsl)
-    psl->tStarts[oBlk] = psl->tStarts[iBlk];  // already in NA coords
-else
-    psl->tStarts[oBlk] = 3 * psl->tStarts[iBlk];
-psl->match += psl->blockSizes[oBlk];
-
-if (oBlk > 0)
-    trimOverlapping(isProtNaPsl, psl, oBlk);
-
-// only advance if something left in the block
-if (psl->blockSizes[oBlk] > 0)
-    oBlk++;
-return oBlk;
-}
-
-static void pslConvertCoords(struct psl *psl)
-/* convert psl coordinates */
-{
-boolean isProtNaPsl = pslIsProtein(psl);
-// overall sizes and coordinates
-psl->qSize *= 3;
-psl->qStart *= 3;
-psl->qEnd *= 3;
-if (!isProtNaPsl)
-    {
-    psl->tSize *= 3;
-    psl->tStart *= 3;
-    psl->tEnd *= 3;
-    }
-
-/* set counts to be all match, since we don't know actual answer and
- * it makes it easier to trim overlapping blocks  */
-psl->match = psl->misMatch = psl->repMatch = psl->nCount = 0;
-
-// blocks
-int oBlk = 0;
-for (int iBlk = 0; iBlk < psl->blockCount; iBlk += 1)
-    {
-    oBlk = updateBlk(isProtNaPsl, psl, iBlk, oBlk);
-    }
-psl->blockCount = oBlk;
-
-// need to update overall coordinates if last block was full remove due to
-// overlap
-psl->qStart = psl->qStarts[0];
-psl->qEnd = psl->qStarts[oBlk - 1] + psl->blockSizes[oBlk - 1];
-if (psl->strand[0] == '-')
-    reverseIntRange(&psl->qStart, &psl->qEnd, psl->qSize);
-psl->tStart = psl->tStarts[0];
-psl->tEnd = psl->tStarts[oBlk - 1] + psl->blockSizes[oBlk - 1];
-if (psl->strand[0] == '-')
-    reverseIntRange(&psl->tStart, &psl->tEnd, psl->tSize);
-
-// indels
-pslComputeInsertCounts(psl);
-}
-
-
 static void pslProtToRnaCoords(char *inPsl, char *outPsl)
 /* pslProtToRnaCoords - Convert protein alignments to RNA coordinates. */
 {
 struct lineFile *inFh = pslFileOpen(inPsl);
 FILE *outFh = mustOpen(outPsl, "w");
 
 struct psl *psl;
 while ((psl = pslNext(inFh)) != NULL)
     {
-    pslConvertCoords(psl);
+    pslProtToNAConvert(psl);
     pslTabOut(psl, outFh);
     pslFree(&psl);
     }
 
 carefulClose(&outFh);
 lineFileClose(&inFh);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 pslProtToRnaCoords(argv[1], argv[2]);
 return 0;
 }