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/pslTransMap.h src/inc/pslTransMap.h
index f8a2928..142d157 100644
--- src/inc/pslTransMap.h
+++ src/inc/pslTransMap.h
@@ -1,28 +1,31 @@
 /* pslTransMap - transitive mapping of an alignment another sequence, via a
  * common alignment */
 #ifndef PSLTRANSMAP_H
 #define PSLTRANSMAP_H
 
 enum pslType
 /* type of PSL needed protein coordinate conversion */
 {
     // n.b. order must match pslTypeDesc
     pslTypeUnspecified = 0,  /* not specified */
     pslTypeProtProt    = 1,  /* protein to protein */
     pslTypeProtNa      = 2,  /* protein to nucleic acid */
     pslTypeNaNa        = 3   /* NA to NA */
 };
 
 enum pslTransMapOpts
 /* option set for pslTransMap */
 {
     pslTransMapNoOpts        = 0x00,   /* no options */
     pslTransMapKeepTrans     = 0x01    /* keep translated alignment strand */
 };
 
 struct psl* pslTransMap(unsigned opts, struct psl *inPsl, enum pslType inPslType,
                         struct psl *mapPsl, enum pslType mapPslType);
 /* map a psl via a mapping psl, a single psl is returned, or NULL if it
  * couldn't be mapped. */
 
+void pslProtToNAConvert(struct psl *psl);
+/* convert a protein/NA or protein/protein alignment to a NA/NA alignment */
+
 #endif