@@ -184,6 +184,7 @@ export(
 
     ## combine_germline_dbs.R:
     combine_germline_dbs,
+    combine_c_region_dbs,
 
     ## augment_germline_db.R:
     augment_germline_db_V,
 
@@ -1,27 +1,65 @@
 ### =========================================================================
-### combine_germline_dbs()
+### combine_germline_dbs() & combine_c_region_dbs()
 ### -------------------------------------------------------------------------
 ###
 
 
+.check_comb_db_name <- function(db_name)
+{
+    if (!isSingleNonWhiteString(db_name))
+        stop(wmsg("'db_name' must be a single (non-empty) string"))
+    if (has_whitespace(db_name))
+        stop(wmsg("'db_name' cannot contain whitespace characters"))
+    if (!has_prefix(db_name, "comb"))
+        stop(wmsg("'db_name' must start with \"comb\""))
+}
+
+.check_suffixes <- function(suffix1, suffix2)
+{
+    if (!isSingleString(suffix1))
+        stop(wmsg("'suffix1' must be a single string"))
+    if (has_whitespace(suffix1))
+        stop(wmsg("'suffix1' cannot contain whitespace characters"))
+    if (!isSingleString(suffix2))
+        stop(wmsg("'suffix2' must be a single string"))
+    if (has_whitespace(suffix2))
+        stop(wmsg("'suffix2' cannot contain whitespace characters"))
+    if (suffix1 == suffix2)
+        stop(wmsg("'suffix1' and 'suffix2' must be different"))
+}
+
+.stop_on_colliding_allele_names <- function()
+{
+    msg1 <- "Allele name collisions!"
+    msg2 <- c("Even after adding 'suffix1' to the allele names of the first ",
+              "db, and 'suffix2' to the allele names of the second db, some ",
+	      "allele names are still colliding. This can be avoided by using ",
+              "more specific suffixes.")
+    stop(wmsg(msg1), "\n  ", wmsg(msg2))
+}
+
 .combine_locus_alleles <- function(locus, alleles1, alleles2, suffix1, suffix2)
 {
     stopifnot(isSingleNonWhiteString(locus),
               is(alleles1, "DNAStringSet"), is(alleles2, "DNAStringSet"),
-              isSingleNonWhiteString(suffix1), isSingleNonWhiteString(suffix2))
+              isSingleString(suffix1), isSingleString(suffix2))
     locus_alleles1 <- alleles1[substr(names(alleles1), 1L, 3L) == locus]
     locus_alleles2 <- alleles2[substr(names(alleles2), 1L, 3L) == locus]
     ## Add user-supplied suffixes to disambiguate allele names.
     names(locus_alleles1) <- add_suffix(names(locus_alleles1), suffix1)
     names(locus_alleles2) <- add_suffix(names(locus_alleles2), suffix2)
-    c(locus_alleles1, locus_alleles2)
+    locus_alleles <- c(locus_alleles1, locus_alleles2)
+    if (anyDuplicated(names(locus_alleles)))
+        .stop_on_colliding_allele_names()
+    locus_alleles
 }
 
-.combine_region_dbs <- function(destdir, db_name1, db_name2, suffix1, suffix2,
+### We only support combining region dbs for the IG loci at the moment.
+.combine_region_dbs <- function(destdir, db_path1, db_path2, suffix1, suffix2,
                                 region_type, verbose=FALSE)
 {
-    alleles1 <- load_germline_db(db_name1, region_types=region_type)
-    alleles2 <- load_germline_db(db_name2, region_types=region_type)
+    alleles1 <- readDNAStringSet(get_db_fasta_file(db_path1, region_type))
+    alleles2 <- readDNAStringSet(get_db_fasta_file(db_path2, region_type))
     loci1 <- substr(names(alleles1), 1, 3)
     loci2 <- substr(names(alleles2), 1, 3)
     stopifnot(all(loci1 %in% IG_LOCI), all(loci2 %in% IG_LOCI))
@@ -33,21 +71,36 @@
 
     locus2alleles <- locus2alleles[lengths(locus2alleles) != 0L]
     stopifnot(length(locus2alleles) != 0L)
-    names(locus2alleles) <- paste0(names(locus2alleles), region_type, ".fasta")
 
-    fasta_files <- vapply(locus2alleles,
-        function(alleles) {
+    loci <- names(locus2alleles)
+    fasta_files <- vapply(loci,
+        function(locus) {
+            alleles <- locus2alleles[[locus]]
             fasta_file <- tempfile(fileext=".fasta")
             writeXStringSet(alleles, fasta_file)
+            if (verbose) {
+                msg <- c("Combined and saved ", length(alleles), " ",
+                         region_type, " alleles for locus ", locus, " to ",
+                         "temp file ", basename(fasta_file))
+                message(wmsg(msg))
+            }
             fasta_file
         },
         character(1))
+    if (verbose)
+        message("")
+    on.exit(unlink(fasta_files))
 
+    names(fasta_files) <- paste0(loci, region_type, ".fasta")
     create_region_db(fasta_files, destdir, region_type=region_type,
                      verbose=verbose)
-    lapply(fasta_files, nuke_file)
 }
 
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### combine_germline_dbs()
+###
+
 .combine_db_intdata <- function(destdir, db_name1, db_name2, suffix1, suffix2,
                                 verbose=FALSE)
 {
@@ -81,49 +134,32 @@
 }
 
 .do_combine_germline_dbs <- function(destdir,
-                                     db_name1, db_name2, suffix1, suffix2,
+                                     db_path1, db_path2, suffix1, suffix2,
                                      verbose=FALSE)
 {
-    if (!isSingleNonWhiteString(db_name1))
-        stop(wmsg("'db_name1' must be a single (non-empty) string"))
-    if (!isSingleNonWhiteString(db_name2))
-        stop(wmsg("'db_name2' must be a single (non-empty) string"))
-    if (!isSingleString(suffix1))
-        stop(wmsg("'suffix1' must be a single string"))
-    if (has_whitespace(suffix1))
-        stop(wmsg("'suffix1' cannot contain whitespace characters"))
-    if (!isSingleString(suffix2))
-        stop(wmsg("'suffix2' must be a single string"))
-    if (has_whitespace(suffix2))
-        stop(wmsg("'suffix2' cannot contain whitespace characters"))
     for (region_type in VDJ_REGION_TYPES)
-        .combine_region_dbs(destdir, db_name1, db_name2, suffix1, suffix2,
+        .combine_region_dbs(destdir, db_path1, db_path2, suffix1, suffix2,
                             region_type, verbose=verbose)
+    db_name1 <- basename(db_path1)
+    db_name2 <- basename(db_path2)
     .combine_db_intdata(destdir, db_name1, db_name2, suffix1, suffix2,
                         verbose=verbose)
     .combine_db_auxdata(destdir, db_name1, db_name2, suffix1, suffix2,
                         verbose=verbose)
 }
 
-
-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### combine_germline_dbs()
-###
-
-### Combine two existing germline dbs, typically from two different
-### organisms, into one hybrid germline db.
+### Combine two existing germline dbs, typically (but not necessarily) from
+### two different organisms, into one hybrid germline db.
 ### Note that allele names are usually not unique across species.
 ### Arguments 'suffix1' and 'suffix2' can be used to disambiguate them.
 combine_germline_dbs <- function(db_name,
                                  db_name1, db_name2, suffix1, suffix2,
                                  overwrite=FALSE, verbose=FALSE)
 {
-    if (!isSingleNonWhiteString(db_name))
-        stop(wmsg("'db_name' must be a single (non-empty) string"))
-    if (has_whitespace(db_name))
-        stop(wmsg("'db_name' cannot contain whitespace characters"))
-    if (!has_prefix(db_name, "comb"))
-        stop(wmsg("'db_name' must start with \"comb\""))
+    .check_comb_db_name(db_name)
+    check_germline_db_name(db_name1, what="'db_name1'")
+    check_germline_db_name(db_name2, what="'db_name2'")
+    .check_suffixes(suffix1, suffix2)
 
     if (!isTRUEorFALSE(overwrite))
         stop(wmsg("'overwrite' must be TRUE or FALSE"))
@@ -132,7 +168,10 @@ combine_germline_dbs <- function(db_name,
 
     db_path <- get_germline_db_path(db_name)
     if (dir.exists(db_path) && !overwrite)
-        stop_on_existing_cached_germline_db(db_name)
+        stop_on_existing_germline_db(db_name)
+
+    db_path1 <- get_germline_db_path(db_name1)
+    db_path2 <- get_germline_db_path(db_name2)
 
     ## We first create the combined germline db in a temporary folder, and,
     ## only if successful, we replace 'db_path' with the temporary folder.
@@ -142,10 +181,55 @@ combine_germline_dbs <- function(db_name,
     tmp_destdir <- tempfile("germline_db_")
     dir.create(tmp_destdir)
     on.exit(nuke_file(tmp_destdir))
-    .do_combine_germline_dbs(tmp_destdir, db_name1, db_name2, suffix1, suffix2,
+    .do_combine_germline_dbs(tmp_destdir, db_path1, db_path2, suffix1, suffix2,
                              verbose=verbose)
     rename_file(tmp_destdir, db_path, replace=TRUE)
 
     invisible(db_name)
 }
 
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### combine_c_region_dbs()
+###
+
+### Combine two existing C-region dbs, typically (but not necessarily) from
+### two different organisms, into one hybrid C-region db.
+### Note that allele names are usually not unique across species.
+### Arguments 'suffix1' and 'suffix2' can be used to disambiguate them.
+combine_c_region_dbs <- function(db_name,
+                                 db_name1, db_name2, suffix1, suffix2,
+                                 overwrite=FALSE, verbose=FALSE)
+{
+    .check_comb_db_name(db_name)
+    check_c_region_db_name(db_name1, what="'db_name1'")
+    check_c_region_db_name(db_name2, what="'db_name2'")
+    .check_suffixes(suffix1, suffix2)
+
+    if (!isTRUEorFALSE(overwrite))
+        stop(wmsg("'overwrite' must be TRUE or FALSE"))
+    if (!isTRUEorFALSE(verbose))
+        stop(wmsg("'verbose' must be TRUE or FALSE"))
+
+    db_path <- get_c_region_db_path(db_name)
+    if (dir.exists(db_path) && !overwrite)
+        stop_on_existing_c_region_db(db_name)
+
+    db_path1 <- get_c_region_db_path(db_name1)
+    db_path2 <- get_c_region_db_path(db_name2)
+
+    ## We first create the combined C-region db in a temporary folder, and,
+    ## only if successful, we replace 'db_path' with the temporary folder.
+    ## Otherwise we destroy the temporary folder and raise an error. This
+    ## achieves atomicity and avoids loosing the content of the existing
+    ## 'db_path' in case something goes wrong.
+    tmp_destdir <- tempfile("c_region_db_")
+    dir.create(tmp_destdir)
+    on.exit(nuke_file(tmp_destdir))
+    .combine_region_dbs(tmp_destdir, db_path1, db_path2, suffix1, suffix2,
+                        "C", verbose=verbose)
+    rename_file(tmp_destdir, db_path, replace=TRUE)
+
+    invisible(db_name)
+}
+
@@ -6,6 +6,20 @@
 ###
 
 
+.LIST_C_REGION_DB_TIP <- c(
+    "Use list_c_region_dbs() to list all the C-region dbs ",
+    "currently installed in the cache (see '?list_c_region_dbs')."
+)
+
+stop_on_existing_c_region_db <- function(db_name)
+{
+    msg1 <- c("C-region db ", db_name, " is already installed ",
+              "in igblastr's persistent cache.")
+    msg3 <- c("Use 'overwrite=TRUE' to reinstall.")
+    stop(wmsg(msg1), "\n  ", wmsg(.LIST_C_REGION_DB_TIP), "\n  ", wmsg(msg3))
+}
+
+
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### list_loci_in_c_region_fasta_dir()
 ###
@@ -59,16 +73,6 @@ list_loci_in_c_region_fasta_dir <- function(fasta_dir, loci_prefix)
 ### create_c_region_db()
 ###
 
-.stop_on_existing_c_region_db <- function(destdir)
-{
-    db_name <- basename(destdir)
-    msg1 <- c("C-region db ", db_name, " is already installed.")
-    msg2 <- c("Use list_c_region_dbs() to list the C-region databases ",
-              "already installed on your machine (see '?list_c_region_dbs').")
-    msg3 <- c("Use 'overwrite=TRUE' to reinstall.")
-    stop(wmsg(msg1), "\n  ", wmsg(msg2), "\n  ", wmsg(msg3))
-}
-
 ### Creates a C-region db (constant regions) from a collection of FASTA
 ### files (typically obtained from IMGT) for a given organism.
 ### Note that 'destdir' will typically be the path to a subdir of the
@@ -93,7 +97,7 @@ create_c_region_db <- function(fasta_dir, loci, destdir,
     }
 
     if (dir.exists(destdir) && !overwrite)
-        .stop_on_existing_c_region_db(destdir)
+        stop_on_existing_c_region_db(basename(destdir))
 
     fasta_files <- .collect_C_fasta_files(fasta_dir, loci)
 
 
@@ -62,7 +62,7 @@
 .load_allele_set <- function(fasta_files, region_type,
                              excluded_alleles=character(0), verbose=FALSE)
 {
-    .checkarg_fasta_files(fasta_files)
+    loci <- .infer_loci_from_filenames(fasta_files, region_type)
     stopifnot(is.character(excluded_alleles), isTRUEorFALSE(verbose))
 
     if (verbose) {
@@ -71,7 +71,6 @@
         message("  o ", wmsg(msg, margin=4L), " ", appendLF=FALSE)
     }
 
-    loci <- .infer_loci_from_filenames(fasta_files, region_type)
     allele_sets <- lapply(seq_along(fasta_files),
         function(i) {
             allele_set <- readDNAStringSet(fasta_files[[i]])
@@ -284,7 +283,7 @@
 .write_region_db <-
     function(cleaned_allele_set, destdir, region_type,
              fasta_files, DORsummary, excluded_alleles=character(0),
-	     verbose=FALSE)
+             verbose=FALSE)
 {
     stopifnot(is.data.frame(DORsummary))
     suffix <- DORsummary[ , "suffix"]
@@ -351,7 +350,7 @@ create_region_db <- function(fasta_files, destdir,
                          disambiguate.allele.names=disambiguate.allele.names,
                          summary.only=TRUE)
     .write_region_db(cleaned_allele_set, destdir, region_type,
-		     fasta_files, DORsummary, excluded_alleles=excluded_alleles,
+                     fasta_files, DORsummary, excluded_alleles=excluded_alleles,
                      verbose=verbose)
 }
 
@@ -412,7 +411,7 @@ create_V_region_db <- function(fasta_files, destdir,
                            disambiguate.allele.names=disambiguate.allele.names,
                            summary.only=TRUE)
     .write_region_db(cleaned_allele_set, destdir, "V",
-		     fasta_files, DORsummary,
+                     fasta_files, DORsummary,
                      verbose=verbose)
     if (with.intdata) {
         if (verbose)
 
@@ -3,23 +3,24 @@
 ### -------------------------------------------------------------------------
 
 
-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### install_germline_db()
-###
-
 .LIST_GERMLINE_DB_TIP <- c(
     "Use list_germline_dbs() to list all the germline dbs ",
     "currently installed in the cache (see '?list_germline_dbs')."
 )
 
-stop_on_existing_cached_germline_db <- function(db_name)
+stop_on_existing_germline_db <- function(db_name)
 {
     msg1 <- c("Germline db ", db_name, " is already installed ",
               "in igblastr's persistent cache.")
     msg3 <- c("Use 'overwrite=TRUE' to reinstall.")
     stop(wmsg(msg1), "\n  ", wmsg(.LIST_GERMLINE_DB_TIP), "\n  ", wmsg(msg3))
 }
 
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### install_germline_db()
+###
+
 .install_germline_db_succeeded <- function(db_name)
 {
     message(wmsg("Germline db ", db_name, " successfully installed ",
@@ -86,7 +87,7 @@ install_germline_db <- function(install_dir, db_name, fasta_dir, loci,
         if (if.exists == "no-op")
             return()
         if (if.exists == "error")
-            stop_on_existing_cached_germline_db(db_name)
+            stop_on_existing_germline_db(db_name)
     }
 
     if (verbose) {