0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55
angie
  Fri Jun 2 11:40:19 2023 -0700
Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.

diff --git src/hg/hgPhyloPlace/phyloPlace.c src/hg/hgPhyloPlace/phyloPlace.c
index 1ee63b4..c44cc02 100644
--- src/hg/hgPhyloPlace/phyloPlace.c
+++ src/hg/hgPhyloPlace/phyloPlace.c
@@ -2923,30 +2923,35 @@
 struct tempName *vcfTn = NULL;
 struct slName *sampleIds = NULL;
 char *usherPath = getUsherPath(TRUE);
 char *protobufPath = NULL;
 char *source = NULL;
 char *metadataFile = NULL;
 char *aliasFile = NULL;
 char *sampleNameFile = NULL;
 struct treeChoices *treeChoices = loadTreeChoices(db);
 getProtobufMetadataSource(db, treeChoices, defaultProtobuf,
                           &protobufPath, &metadataFile, &source, &aliasFile, &sampleNameFile);
 reportTiming(&startTime, "start up and find the tree etc. files");
 struct mutationAnnotatedTree *bigTree = NULL;
 lineFileCarefulNewlines(lf);
 char *chrom = hDefaultChrom(db);
+//#*** Hack for influenza
+if (stringIn("GCF_000865085.1", db))
+    chrom = "NC_007366.1";
+else if (stringIn("GCF_001343785.1", db))
+    chrom = "NC_026433.1";
 int chromSize = hChromSize(db, chrom);
 struct slName **maskSites = getProblematicSites(db, chrom, chromSize);
 //#*** TODO: add CGI param option for this almost-never-needed tweak:
 if (0)
     {
     bigTree = parseParsimonyProtobuf(protobufPath);
     reportTiming(&startTime, "parse protobuf file (at startup, for excluding informativeBases "
                  "from maskSites)");
     informativeBasesFromTree(bigTree->tree, maskSites, chromSize);
     reportTiming(&startTime, "remove any informative bases in tree from maskSites");
     }
 struct dnaSeq *refGenome = hChromSeq(db, chrom, 0, chromSize);
 boolean isFasta = FALSE;
 boolean subtreesOnly = FALSE;
 struct seqInfo *seqInfoList = NULL;