diff --git a/Cargo.lock b/Cargo.lock
index a8b08bfda..fd0b11c7a 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -35,7 +35,7 @@ dependencies = [
 [[package]]
 name = "align_tools"
 version = "0.1.12"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "bio_edit",
  "debruijn",
@@ -47,7 +47,7 @@ dependencies = [
 [[package]]
 name = "amino"
 version = "0.1.7"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "debruijn",
  "string_utils",
@@ -56,7 +56,7 @@ dependencies = [
 [[package]]
 name = "ansi_escape"
 version = "0.1.3"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "string_utils",
  "vector_utils",
@@ -248,7 +248,7 @@ dependencies = [
 [[package]]
 name = "bio_edit"
 version = "0.1.1"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "bio-types",
  "bit-set",
@@ -624,7 +624,7 @@ dependencies = [
 [[package]]
 name = "dna"
 version = "0.1.3"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 
 [[package]]
 name = "doc-comment"
@@ -647,7 +647,7 @@ checksum = "e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457"
 [[package]]
 name = "enclone"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "amino",
  "ansi_escape",
@@ -672,7 +672,7 @@ dependencies = [
 [[package]]
 name = "enclone_args"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "debruijn",
  "enclone_core",
@@ -708,7 +708,7 @@ dependencies = [
 [[package]]
 name = "enclone_core"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "amino",
  "ansi_escape",
@@ -852,7 +852,7 @@ dependencies = [
 [[package]]
 name = "enclone_print"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "amino",
  "ansi_escape",
@@ -884,7 +884,7 @@ dependencies = [
 [[package]]
 name = "enclone_proto"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "bio_edit",
  "byteorder",
@@ -897,7 +897,7 @@ dependencies = [
 [[package]]
 name = "enclone_ranger"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "enclone",
  "enclone_args",
@@ -913,7 +913,7 @@ dependencies = [
 [[package]]
 name = "enclone_stuff"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "amino",
  "debruijn",
@@ -1018,7 +1018,7 @@ dependencies = [
 [[package]]
 name = "enclone_vars"
 version = "0.5.219"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "io_utils",
  "itertools",
@@ -1057,7 +1057,7 @@ dependencies = [
 [[package]]
 name = "equiv"
 version = "0.1.3"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 
 [[package]]
 name = "errno"
@@ -1099,7 +1099,7 @@ checksum = "1d4fd7bd9e32c1205549decf6f36772d7b606a579b26afaffa335ae148151a5d"
 [[package]]
 name = "exons"
 version = "0.1.5"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "io_utils",
  "string_utils",
@@ -1109,7 +1109,7 @@ dependencies = [
 [[package]]
 name = "expr_tools"
 version = "0.1.3"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "evalexpr",
  "statrs",
@@ -1120,7 +1120,7 @@ dependencies = [
 [[package]]
 name = "fasta_tools"
 version = "0.1.8"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "debruijn",
  "flate2",
@@ -1284,7 +1284,7 @@ checksum = "6fb8d784f27acf97159b40fc4db5ecd8aa23b9ad5ef69cdd136d3bc80665f0c0"
 [[package]]
 name = "graph_simple"
 version = "0.1.5"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "petgraph",
  "vector_utils",
@@ -1329,7 +1329,7 @@ name = "hdf5-sys"
 version = "0.8.1"
 source = "git+https://github.com/10XGenomics/hdf5-rust.git?branch=conda_nov2021#2d4a40b7ef75de530bc53fd2eb0fe75047e083ad"
 dependencies = [
- "attohttpc 0.18.0",
+ "attohttpc 0.19.1",
  "bzip2",
  "libc",
  "libloading",
@@ -1391,7 +1391,7 @@ dependencies = [
 [[package]]
 name = "hyperbase"
 version = "0.1.8"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "debruijn",
  "equiv",
@@ -1425,7 +1425,7 @@ dependencies = [
 [[package]]
 name = "io_utils"
 version = "0.3.2"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "bincode",
  "flate2",
@@ -1491,7 +1491,7 @@ dependencies = [
 [[package]]
 name = "kmer_lookup"
 version = "0.1.5"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "debruijn",
  "rayon",
@@ -2544,12 +2544,12 @@ dependencies = [
 [[package]]
 name = "stats_utils"
 version = "0.1.3"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 
 [[package]]
 name = "string_utils"
 version = "0.1.4"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "vector_utils",
 ]
@@ -2613,7 +2613,7 @@ dependencies = [
 [[package]]
 name = "tables"
 version = "0.1.5"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "io_utils",
  "itertools",
@@ -2903,7 +2903,7 @@ dependencies = [
 [[package]]
 name = "vdj_ann"
 version = "0.4.4"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "align_tools",
  "amino",
@@ -2925,7 +2925,7 @@ dependencies = [
 [[package]]
 name = "vdj_ann_ref"
 version = "0.2.1"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "debruijn",
  "exons",
@@ -2941,7 +2941,7 @@ dependencies = [
 [[package]]
 name = "vdj_types"
 version = "0.2.0"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "serde",
 ]
@@ -2958,7 +2958,7 @@ dependencies = [
 [[package]]
 name = "vector_utils"
 version = "0.1.5"
-source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/break-up-annotation#8bf91912c3032c154ba72e4596f6811a19d0c634"
+source = "git+https://github.com/10XGenomics/enclone_ranger?branch=macklin/collapse-annotation-helper-types#4b954d77ae678c6a593094c990904c19bf8b7b1b"
 dependencies = [
  "permutation",
  "superslice",
diff --git a/Cargo.toml b/Cargo.toml
index 83d63057c..bc02ccc9d 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -63,19 +63,19 @@ split-debuginfo = "unpacked"
 # improved.
 
 [workspace.dependencies]
-align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+align_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+amino = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 anyhow = "1"
-ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+ansi_escape = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 arboard = "2"
 assert_cmd = "2"
 async-trait = "0.1"
 attohttpc = { version = "0.18", default-features = false, features = ["compress", "tls-rustls"] }
 backtrace = "0.3"
 base64 = "0.13"
-binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+binary_vec_io = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 bio = "0.39"
-bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+bio_edit = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 byteorder = "1"
 bytes = "1"
 chrono = { version = "0.4", default-features = false, features = ["std", "clock"] }
@@ -86,41 +86,41 @@ core-graphics = "0.22"
 crc = "2"
 debruijn = "0.3"
 dirs = "4"
-dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+dna = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 edit-distance = "2"
-enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+enclone_args = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+enclone_core = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 enclone_denovo = { path = "../enclone_denovo" }
 enclone_help = { path = "../enclone_help" }
-enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+enclone = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+enclone_print = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+enclone_proto = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+enclone_ranger = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 enclone_server_proto = { path = "../enclone_server_proto" }
-enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+enclone_stuff = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 enclone_tail = { path = "../enclone_tail" }
-enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+enclone_vars = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 enclone_version = { path = "../enclone_version" }
-equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+equiv = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 evalexpr = "7"
-expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+expr_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+fasta_tools = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 file-lock = "2"
 flate2 = "1"
 float-ord = "0.3"
 fontdb = "0.7"
 fs_extra = "1"
 git = "https://github.com/10xGenomics/hdf5-rust.git"
-graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+graph_simple = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 hdf5 = { git = "https://github.com/10XGenomics/hdf5-rust.git", branch = "conda_nov2021", features = ["conda"], default-features = false }
 home = "0.5"
-hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+hyperbase = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 image = { version = "0.23", features = ["jpeg", "png", "jpeg_rayon"], default-features = false }
 include_dir = { version = "0.6", features = ["search"] }
-io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+io_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 itertools = "0.10"
 jpeg-decoder = "0.2"
-kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+kmer_lookup = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 lazy_static = "1"
 libc = "0.2"
 log = "0.4"
@@ -133,7 +133,7 @@ num-traits = "0.2"
 objc = "0.2"
 pager = "0.16"
 palette = "0.6"
-perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+perf_stats = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 permutation = "0.4"
 petgraph = "0.6"
 plotters = { version = "0.3", default_features = false, features = ["svg_backend", "point_series"] }
@@ -154,12 +154,12 @@ serde = "1"
 serde_derive = "1"
 serde_json = "1"
 sha2 = "0.10"
-stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+stats_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 statrs = "0.15"
-stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+stirling_numbers = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+string_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 superslice = "1"
-tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+tables = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 tar = "0.4"
 thiserror = "1"
 tilde-expand = "0.1"
@@ -171,9 +171,9 @@ tonic-build = { version = "0.6", default-features = false, features = ["transpor
 triple_accel = "0.4"
 users = "0.11"
 usvg = { version = "0.19", features = ["text"] }
-vdj_types = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
-vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/break-up-annotation" }
+vdj_types = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+vdj_ann = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+vdj_ann_ref = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
+vector_utils = { git = "https://github.com/10XGenomics/enclone_ranger", branch = "macklin/collapse-annotation-helper-types" }
 whoami = "1"
 yaml-rust = "0.4"
diff --git a/enclone_paper/src/bin/olga_splice.rs b/enclone_paper/src/bin/olga_splice.rs
index 5691a6a5a..f3ecea71f 100644
--- a/enclone_paper/src/bin/olga_splice.rs
+++ b/enclone_paper/src/bin/olga_splice.rs
@@ -204,8 +204,7 @@ fn main() {
         fwriteln!(log, "\ncdr3[{}] = {}\n", i + 1, cdr3[i]);
         fwriteln!(log, "seq[{}] = {}\n", i + 1, strme(&seq));
         let x = DnaString::from_dna_string(strme(&seq));
-        let mut ann = Vec::<Annotation>::new();
-        annotate_seq(&x, &refdata, &mut ann, true, false, true);
+        let ann = annotate_seq(&x, &refdata, true, false, true);
         let mut annv = Vec::<Annotation>::new();
         for i in 0..ann.len() {
             let t = ann[i].ref_id as usize;
diff --git a/enclone_tools/src/bin/annotate_seq.rs b/enclone_tools/src/bin/annotate_seq.rs
index 1f09e5e15..910d04565 100644
--- a/enclone_tools/src/bin/annotate_seq.rs
+++ b/enclone_tools/src/bin/annotate_seq.rs
@@ -134,8 +134,7 @@ fn main() {
             fwriteln!(log, "\nFW ANNOTATION VERSUS PLAIN REFERENCE\n");
         }
         print_annotations(&seq, &refdata, &mut log, false, true, verbose);
-        let mut ann = Vec::<Annotation>::new();
-        annotate_seq(&seq, &refdata, &mut ann, true, false, true);
+        let ann = annotate_seq(&seq, &refdata, true, false, true);
         print_cdr3_using_ann(&seq, &refdata, &ann, &mut log);
         print_start_codon_positions(&seq, &mut log);
         if is_productive_contig(&seq, &refdata, &ann).0 {
diff --git a/enclone_tools/src/bin/annotate_seqs.rs b/enclone_tools/src/bin/annotate_seqs.rs
index 6963362bc..682bd7800 100644
--- a/enclone_tools/src/bin/annotate_seqs.rs
+++ b/enclone_tools/src/bin/annotate_seqs.rs
@@ -76,8 +76,7 @@ fn main() {
         let mut log = Vec::<u8>::new();
         fwriteln!(log, ", len = {}", len);
         print_annotations(&seq, &refdata, &mut log, false, true, false);
-        let mut ann = Vec::<Annotation>::new();
-        annotate_seq(&seq, &refdata, &mut ann, true, false, true);
+        let ann = annotate_seq(&seq, &refdata, true, false, true);
         let (valid, _) = is_productive_contig(&seq, &refdata, &ann);
         let mut shift = false;
         for i in 1..ann.len() {