834653e22227fcea282e12a48910bb73068b34df
angie
  Mon Apr 29 15:33:06 2024 -0700
Don't depend on having a PSL alignment for the results table, precompute the same values whether aligning with gf/blat or nextclade.

diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h
index 9578617..fabc6b0 100644
--- src/hg/hgPhyloPlace/phyloPlace.h
+++ src/hg/hgPhyloPlace/phyloPlace.h
@@ -46,42 +46,44 @@
 {
     char **protobufFiles;      // Mutation annotated tree files in protobuf format for UShER
     char **metadataFiles;      // Sample metadata a la GISAID's nextmeta download option
     char **sources;            // GISAID or public
     char **descriptions;       // Menu labels to describe the options to the user
     char **aliasFiles;         // Two-column files associating IDs/aliases with full tree names
     char **sampleNameFiles;    // One-column files with full tree names
     int count;                 // Number of choices (and size of each array)
 };
 
 struct seqInfo
 /* User sequences, alignments and statistics */
 {
     struct seqInfo *next;
     struct dnaSeq *seq;                     // Uploaded sequence
-    struct psl *psl;                        // Alignment to reference (if FASTA uploaded)
     struct singleNucChange *sncList;        // SNVs in seq
     struct singleNucChange *maskedSncList;  // SNVs that were masked (not used for placement)
     struct slRef *maskedReasonsList;        // Reason (from Problematic Sites) for masking each SNV
     uint nCountStart;                       // #Ns at beginning of seq
     uint nCountMiddle;                      // #Ns not at beginning or end of seq
     uint nCountEnd;                         // #Ns at end of seq
     uint ambigCount;                        // # ambiguous IUPAC bases
     char *insRanges;                        // ranges and sequences inserted into reference
     char *delRanges;                        // ranges and sequences deleted from reference
     uint insBases;                          // total #bases inserted into reference
     uint delBases;                          // total #bases deleted from reference
+    uint basesAligned;                      // number of bases aligned to reference
+    uint tStart;                            // alignment start in reference
+    uint tEnd;                              // alignment end in reference
 };
 
 struct variantPathNode
 /* A list of these gives a path from phylo tree root to some node (usually user seq leaf). */
     {
     struct variantPathNode *next;
     char *nodeName;                   // Either a numeric internal node ID or the user seq name
     struct singleNucChange *sncList;  // One or more single nucleotide changes associated with node
     };
 
 struct baseVal
 /* List of imputed base positions and values */
     {
     struct baseVal *next;
     int chromStart;         // 0-based position