a97f8a0fffb31a2b3521e573a03f454fb60275d3
markd
  Tue May 30 21:30:12 2023 -0700
Add mechnaism to fix problem with mapping prot-prot via prot-na alignment by explictly specifying the type of alignments

diff --git src/inc/pslTransMap.h src/inc/pslTransMap.h
index 0f53035..f8a2928 100644
--- src/inc/pslTransMap.h
+++ src/inc/pslTransMap.h
@@ -1,17 +1,28 @@
 /* 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, struct psl *mapPsl);
+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. */
 
 #endif