@@ -2,7 +2,7 @@ Type: Package

 Package: CellaRepertorium

 Title: Data structures, clustering and testing for single 

     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

-Version: 1.3.0

+Version: 1.3.1

 Authors@R: 

     c(person(given = "Andrew",

              family = "McDavid",

@@ -72,7 +72,7 @@ VignetteBuilder:

     knitr

 Encoding: UTF-8

 NeedsCompilation: yes

-RoxygenNote: 7.1.1

+RoxygenNote: 7.1.2

 URL: https://github.com/amcdavid/CellaRepertorium

 BugReports: https://github.com/amcdavid/CellaRepertorium/issues

 Roxygen: list(markdown = TRUE)

@@ -151,7 +151,7 @@ cland = function(X, Y, new_pk){

                             Y$contig_tbl[c(Y$cluster_pk, Y$contig_pk)], join = dplyr::inner_join, by = X$contig_pk, overwrite = FALSE)

     contigs[[new_pk]] = interaction(contigs[[X$cluster_pk]], contigs[[Y$cluster_pk]])

     # I guess we have mostly been an integer, otherwise ?

-    contigs[[new_pk]] = as.numeric(as.character(factor(contigs[[new_pk]], labels = seq_along(unique(contigs[[new_pk]])))))

+    contigs[[new_pk]] = as.integer(factor(contigs[[new_pk]]))

     cluster_tblX = unique(contigs[c(new_pk, X$cluster_pk, Y$cluster_pk)]) %>% left_join_warn(X$cluster_tbl, by = X$cluster_pk, overwrite =  TRUE) %>% left_join_warn(Y$cluster_tbl, by = Y$cluster_pk, overwrite = TRUE)

     cdb = replace_cluster_tbl(X, cluster_tblX, contigs, new_pk, warn = FALSE)

     if (has_fineclustering(cdb)) warning("Rerun `fine_clustering` to update results.")

@@ -5,6 +5,11 @@

 using namespace Rcpp;

+#ifdef RCPP_USE_GLOBAL_ROSTREAM

+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();

+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();

+#endif

+

 // cdhitestC

 IntegerVector cdhitestC(List opts, CharacterVector name, bool showProgress);

 RcppExport SEXP _CellaRepertorium_cdhitestC(SEXP optsSEXP, SEXP nameSEXP, SEXP showProgressSEXP) {