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/inc/psl.h src/inc/psl.h
index 3774681..0cd5090 100644
--- src/inc/psl.h
+++ src/inc/psl.h
@@ -255,30 +255,33 @@
 void pslDump(struct psl *psl, FILE *f);
 /* Dump most of PSL to file - for debugging. */
 
 struct psl *pslTrimToTargetRange(struct psl *oldPsl, int tMin, int tMax);
 /* Return psl trimmed to fit inside tMin/tMax.  Note this does not
  * update the match/misMatch and related fields. */
 
 struct psl *pslTrimToQueryRange(struct psl *oldPsl, int qMin, int qMax);
 /* Return psl trimmed to fit inside qMin/qMax.  Note this does not
  * update the match/misMatch and related fields. */
 
 void pslRecalcBounds(struct psl *psl);
 /* Calculate qStart/qEnd tStart/tEnd at top level to be consistent
  * with blocks. */
 
+void pslRecalcBaseCounts(struct psl *psl);
+/* Update match/mismatch base counts in PSL, assuming everything is a match */
+
 int pslCheck(char *pslDesc, FILE* out, struct psl* psl);
 /* Validate a PSL for consistency.  pslDesc is printed the error messages
  * to file out (open /dev/null to discard). Return count of errors. */
 
 int pslCheck2(unsigned opts, char *pslDesc, FILE* out, struct psl* psl);
 /* Validate a PSL for consistency.  pslDesc is printed the error messages to
  * file out (open /dev/null to discard). Return count of errors.  Option
  * PSL_CHECK_IGNORE_INSERT_CNTS doesn't validate problems insert counts fields
  * in each PSL.  Useful because protein PSL doesn't seen to compute these in a
  * consistent way.
  */
 
 int pslCountBlocks(struct psl *target, struct psl *query, int maxBlockGap);
 /* count the number of blocks in the query that overlap the target */
 /* merge blocks that are closer than maxBlockGap */