- cigzip (binary, 0.1.0-b7cc0ed) -- successfully packaged and added to pangenomes

  - tracepoints -- library-only Rust crate, already available as rust-tracepoints-0.1.0.66a5511 in pangenome-rust.scm
  for dependency use; cigzip exposes its functionality as a CLI

2 files changed, 505 insertions, 1 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index fffd077..9f5ba8e 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -2333,6 +2333,190 @@
   (crate-source "vcf" "0.6.1"
                 "0dc0p00a19rpmhrqcshrn2qg5l716b5s1fy8vpd3p32bw77vpbs0"))
 
+;; cigzip-specific crates
+(define rust-cc-1.2.60
+  (crate-source "cc" "1.2.60"
+                "084a8ziprdlyrj865f3303qr0b7aaggilkl18slncss6m4yp1ia3"))
+
+
+(define rust-icu-collections-2.2.0
+  (crate-source "icu_collections" "2.2.0"
+                "070r7xd0pynm0hnc1v2jzlbxka6wf50f81wybf9xg0y82v6x3119"))
+
+
+(define rust-icu-locale-core-2.2.0
+  (crate-source "icu_locale_core" "2.2.0"
+                "0a9cmin5w1x3bg941dlmgszn33qgq428k7qiqn5did72ndi9n8cj"))
+
+
+(define rust-icu-normalizer-2.2.0
+  (crate-source "icu_normalizer" "2.2.0"
+                "1d7krxr0xpc4x9635k1100a24nh0nrc59n65j6yk6gbfkplmwvn5"))
+
+(define rust-icu-normalizer-data-2.2.0
+  (crate-source "icu_normalizer_data" "2.2.0"
+                "0f5d5d5fhhr9937m2z6z38fzh6agf14z24kwlr6lyczafypf0fys"))
+
+
+
+(define rust-icu-properties-2.2.0
+  (crate-source "icu_properties" "2.2.0"
+                "1pkh3s837808cbwxvfagwc28cvwrz2d9h5rl02jwrhm51ryvdqxy"))
+
+(define rust-icu-properties-data-2.2.0
+  (crate-source "icu_properties_data" "2.2.0"
+                "052awny0qwkbcbpd5jg2cd7vl5ry26pq4hz1nfsgf10c3qhbnawf"))
+
+
+
+(define rust-icu-provider-2.2.0
+  (crate-source "icu_provider" "2.2.0"
+                "08dl8pxbwr8zsz4c5vphqb7xw0hykkznwi4rw7bk6pwb3krlr70k"))
+
+
+(define rust-js-sys-0.3.95
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "js-sys" "0.3.95"
+                "1jhj3kgxxgwm0cpdjiz7i2qapqr7ya9qswadmr63dhwx3lnyjr19"))
+
+
+(define rust-lib-wfa2-0.1.0.8859b6a
+  ;; TODO REVIEW: Define standalone package if this is a workspace.
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/AndreaGuarracino/lib_wfa2")
+                        (commit "8859b6a214141968f37d9bcb22552408318adda0")))
+    (file-name (git-file-name "rust-lib-wfa2" "0.1.0.8859b6a"))
+    (sha256 (base32 "08hfx5pzcmvk7pnxhjg6nvf77ng9rjrnysynj0qf6n6xd4n02qxa"))))
+
+
+(define rust-libz-sys-1.1.28
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "libz-sys" "1.1.28"
+                "08hyf9v85zifl3353xc7i5wr53v9b3scri856cmphl3gaxp24fpw"))
+
+
+(define rust-litemap-0.8.2
+  (crate-source "litemap" "0.8.2"
+                "1w7628bc7wwcxc4n4s5kw0610xk06710nh2hn5kwwk2wa91z9nlj"))
+
+
+(define rust-pkg-config-0.3.33
+  (crate-source "pkg-config" "0.3.33"
+                "17jnqmcbxsnwhg9gjf0nh6dj5k0x3hgwi3mb9krjnmfa9v435w8r"))
+
+
+(define rust-portable-atomic-util-0.2.7
+  (crate-source "portable-atomic-util" "0.2.7"
+                "0616j0fhy6y71hyxg3n86f6hng0fmsc269s3wp4gl8ww4p8hd8f2"))
+
+
+(define rust-potential-utf-0.1.5
+  (crate-source "potential_utf" "0.1.5"
+                "0r0518fr32xbkgzqap509s3r60cr0iancsg9j1jgf37cyz7b20q1"))
+
+
+(define rust-ragc-common-0.1.1.40e5cad
+  ;; TODO REVIEW: Define standalone package if this is a workspace.
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/ekg/ragc")
+                        (commit "40e5cad11cab7d4df07a72d6b16d68c2d60b0742")))
+    (file-name (git-file-name "rust-ragc-common" "0.1.1.40e5cad"))
+    (sha256 (base32 "1p71jj02ppcvkrvnbs4y0yf00cslzqhlx4idscx8fk4lhmip4kla"))))
+
+
+(define rust-ragc-core-0.1.1.40e5cad
+  ;; TODO REVIEW: Define standalone package if this is a workspace.
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/ekg/ragc")
+                        (commit "40e5cad11cab7d4df07a72d6b16d68c2d60b0742")))
+    (file-name (git-file-name "rust-ragc-core" "0.1.1.40e5cad"))
+    (sha256 (base32 "1p71jj02ppcvkrvnbs4y0yf00cslzqhlx4idscx8fk4lhmip4kla"))))
+
+
+(define rust-tinystr-0.8.3
+  (crate-source "tinystr" "0.8.3"
+                "0vfr8x285w6zsqhna0a9jyhylwiafb2kc8pj2qaqaahw48236cn8"))
+
+
+(define rust-wasm-bindgen-0.2.118
+  (crate-source "wasm-bindgen" "0.2.118"
+                "129s5r14fx4v4xrzpx2c6l860nkxpl48j50y7kl6j16bpah3iy8b"))
+
+(define rust-wasm-bindgen-macro-0.2.118
+  (crate-source "wasm-bindgen-macro" "0.2.118"
+                "1v98r8vs17cj8918qsg0xx4nlg4nxk1g0jd4nwnyrh1687w29zzf"))
+
+(define rust-wasm-bindgen-macro-support-0.2.118
+  (crate-source "wasm-bindgen-macro-support" "0.2.118"
+                "0169jr0q469hfx5zqxfyywf2h2f4aj17vn4zly02nfwqmxghc24x"))
+
+(define rust-wasm-bindgen-shared-0.2.118
+  (crate-source "wasm-bindgen-shared" "0.2.118"
+                "0ag1vvdzi4334jlzilsy14y3nyzwddf1ndn62fyhf6bg62g4vl2z"))
+
+
+
+
+
+(define rust-web-sys-0.3.95
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "web-sys" "0.3.95"
+                "0zfr2jy5bpkkggl88i43yy37p538hg20i56kwn421yj9g6qznbag"))
+
+
+(define rust-writeable-0.6.3
+  (crate-source "writeable" "0.6.3"
+                "1i54d13h9bpap2hf13xcry1s4lxh7ap3923g8f3c0grd7c9fbyhz"))
+
+
+(define rust-yoke-0.8.2
+  (crate-source "yoke" "0.8.2"
+                "1jprcs7a98a5whvfs6r3jvfh1nnfp6zyijl7y4ywmn88lzywbs5b"))
+
+(define rust-yoke-derive-0.8.2
+  (crate-source "yoke-derive" "0.8.2"
+                "13l5y5sz4lqm7rmyakjbh6vwgikxiql51xfff9hq2j485hk4r16y"))
+
+
+
+(define rust-zerocopy-0.8.48
+  (crate-source "zerocopy" "0.8.48"
+                "1sb8plax8jbrsng1jdval7bdhk7hhrx40dz3hwh074k6knzkgm7f"))
+
+(define rust-zerocopy-derive-0.8.48
+  (crate-source "zerocopy-derive" "0.8.48"
+                "1m5s0g92cxggqc74j83k1priz24k3z93sj5gadppd20p9c4cvqvh"))
+
+
+
+(define rust-zerofrom-0.1.7
+  (crate-source "zerofrom" "0.1.7"
+                "1py40in4rirc9q8w36q67pld0zk8ssg024xhh0cncxgal7ra3yk9"))
+
+(define rust-zerofrom-derive-0.1.7
+  (crate-source "zerofrom-derive" "0.1.7"
+                "18c4wsnznhdxx6m80piil1lbyszdiwsshgjrybqcm4b6qic22lqi"))
+
+
+
+(define rust-zerotrie-0.2.4
+  (crate-source "zerotrie" "0.2.4"
+                "1gr0pkcn3qsr6in6iixqyp0vbzwf2j1jzyvh7yl2yydh3p9m548g"))
+
+
+(define rust-zerovec-0.11.6
+  (crate-source "zerovec" "0.11.6"
+                "0fdjsy6b31q9i0d73sl7xjd12xadbwi45lkpfgqnmasrqg5i3ych"))
+
+(define rust-zerovec-derive-0.11.3
+  (crate-source "zerovec-derive" "0.11.3"
+                "0m85qj92mmfvhjra6ziqky5b1p4kcmp5069k7kfadp5hr8jw8pb2"))
+
+
+
 ;; pafplot-specific crates
 (define rust-boomphf-0.6.0
   (crate-source "boomphf" "0.6.0"
@@ -3511,7 +3695,215 @@
           rust-utf8parse-0.2.2
           rust-version-check-0.9.5
           rust-windows-link-0.2.1
-          rust-windows-sys-0.61.2)))
+          rust-windows-sys-0.61.2))
+  (cigzip =>
+    (list rust-adler2-2.0.1
+          rust-ahash-0.8.12
+          rust-aho-corasick-1.1.4
+          rust-allocator-api2-0.2.21
+          rust-anes-0.1.6
+          rust-anstream-1.0.0
+          rust-anstyle-1.0.14
+          rust-anstyle-parse-1.0.0
+          rust-anstyle-query-1.1.5
+          rust-anstyle-wincon-3.0.11
+          rust-anyhow-1.0.102
+          rust-arbitrary-chunks-0.4.1
+          rust-autocfg-1.5.0
+          rust-bgzip-0.3.1
+          rust-bincode-1.3.3
+          rust-bindgen-0.69.5
+          rust-bio-types-1.0.4
+          rust-bitflags-2.11.1
+          rust-block-buffer-0.10.4
+          rust-block-pseudorand-0.1.2
+          rust-bumpalo-3.20.2
+          rust-byteorder-1.5.0
+          rust-bytes-1.11.1
+          rust-cast-0.3.0
+          rust-cc-1.2.60
+          rust-cexpr-0.6.0
+          rust-cfg-if-1.0.4
+          rust-chiapos-chacha8-0.1.0
+          rust-ciborium-0.2.2
+          rust-ciborium-io-0.2.2
+          rust-ciborium-ll-0.2.2
+          rust-clang-sys-1.8.1
+          rust-clap-4.6.1
+          rust-clap-builder-4.6.0
+          rust-clap-derive-4.6.1
+          rust-clap-lex-1.1.0
+          rust-cmake-0.1.58
+          rust-colorchoice-1.0.5
+          rust-console-0.16.3
+          rust-cpufeatures-0.2.17
+          rust-crc32fast-1.5.0
+          rust-criterion-0.5.1
+          rust-criterion-plot-0.5.0
+          rust-crossbeam-0.8.4
+          rust-crossbeam-channel-0.5.15
+          rust-crossbeam-deque-0.8.6
+          rust-crossbeam-epoch-0.9.18
+          rust-crossbeam-queue-0.3.12
+          rust-crossbeam-utils-0.8.21
+          rust-crunchy-0.2.4
+          rust-crypto-common-0.1.7
+          rust-custom-derive-0.1.7
+          rust-dashmap-6.1.0
+          rust-derive-new-0.6.0
+          rust-derive-new-0.7.0
+          rust-digest-0.10.7
+          rust-displaydoc-0.2.5
+          rust-either-1.15.0
+          rust-encode-unicode-1.0.0
+          rust-env-filter-1.0.1
+          rust-env-logger-0.11.10
+          rust-find-msvc-tools-0.1.9
+          rust-flate2-1.1.9
+          rust-form-urlencoded-1.2.2
+          rust-fs-utils-1.1.4
+          rust-generic-array-0.14.7
+          rust-getrandom-0.3.4
+          rust-glob-0.3.3
+          rust-half-2.7.1
+          rust-hashbrown-0.14.5
+          rust-heck-0.5.0
+          rust-hermit-abi-0.5.2
+          rust-hts-sys-2.2.0
+          rust-icu-collections-2.2.0
+          rust-icu-locale-core-2.2.0
+          rust-icu-normalizer-2.2.0
+          rust-icu-normalizer-data-2.2.0
+          rust-icu-properties-2.2.0
+          rust-icu-properties-data-2.2.0
+          rust-icu-provider-2.2.0
+          rust-idna-1.1.0
+          rust-idna-adapter-1.2.1
+          rust-ieee754-0.2.6
+          rust-indicatif-0.18.4
+          rust-is-terminal-0.4.17
+          rust-is-terminal-polyfill-1.70.2
+          rust-itertools-0.10.5
+          rust-itertools-0.12.1
+          rust-itoa-1.0.18
+          rust-jiff-0.2.23
+          rust-jiff-static-0.2.23
+          rust-jobserver-0.1.34
+          rust-js-sys-0.3.95
+          rust-lazy-static-1.5.0
+          rust-lazycell-1.3.0
+          rust-lib-wfa2-0.1.0.8859b6a
+          rust-libc-0.2.185
+          rust-libdeflate-sys-1.25.2
+          rust-libloading-0.8.9
+          rust-libz-sys-1.1.28
+          rust-linear-map-1.2.0
+          rust-litemap-0.8.2
+          rust-lock-api-0.4.14
+          rust-log-0.4.29
+          rust-memchr-2.8.0
+          rust-minimal-lexical-0.2.1
+          rust-miniz-oxide-0.8.9
+          rust-nanorand-0.6.1
+          rust-newtype-derive-0.1.6
+          rust-nom-7.1.3
+          rust-noodles-0.100.0
+          rust-noodles-bgzf-0.42.0
+          rust-num-traits-0.2.19
+          rust-num-cpus-1.17.0
+          rust-once-cell-1.21.4
+          rust-once-cell-polyfill-1.70.2
+          rust-oorandom-11.1.5
+          rust-parking-lot-core-0.9.12
+          rust-partition-0.1.2
+          rust-percent-encoding-2.3.2
+          rust-pkg-config-0.3.33
+          rust-plotters-0.3.7
+          rust-plotters-backend-0.3.7
+          rust-plotters-svg-0.3.7
+          rust-portable-atomic-1.13.1
+          rust-portable-atomic-util-0.2.7
+          rust-potential-utf-0.1.5
+          rust-proc-macro2-1.0.106
+          rust-quick-error-1.2.3
+          rust-quote-1.0.45
+          rust-r-efi-5.3.0
+          rust-ragc-common-0.1.1.40e5cad
+          rust-ragc-core-0.1.1.40e5cad
+          rust-rayon-1.12.0
+          rust-rayon-core-1.13.0
+          rust-rdst-0.20.14
+          rust-redox-syscall-0.5.18
+          rust-regex-1.12.3
+          rust-regex-automata-0.4.14
+          rust-regex-syntax-0.8.10
+          rust-rust-htslib-1.0.0
+          rust-rustc-hash-1.1.0
+          rust-rustc-version-0.1.7
+          rust-rustversion-1.0.22
+          rust-same-file-1.0.6
+          rust-scopeguard-1.2.0
+          rust-semver-0.1.20
+          rust-serde-1.0.228
+          rust-serde-core-1.0.228
+          rust-serde-derive-1.0.228
+          rust-serde-json-1.0.149
+          rust-sha2-0.10.9
+          rust-shlex-1.3.0
+          rust-simd-adler32-0.3.9
+          rust-smallvec-1.15.1
+          rust-stable-deref-trait-1.2.1
+          rust-strsim-0.11.1
+          rust-strum-macros-0.26.4
+          rust-syn-2.0.117
+          rust-synstructure-0.13.2
+          rust-thiserror-1.0.69
+          rust-thiserror-2.0.18
+          rust-thiserror-impl-1.0.69
+          rust-thiserror-impl-2.0.18
+          rust-tikv-jemalloc-sys-0.5.4+5.3.0-patched
+          rust-tikv-jemallocator-0.5.4
+          rust-tinystr-0.8.3
+          rust-tinytemplate-1.2.1
+          rust-tpa-0.1.0.49f1801
+          rust-tracepoints-0.1.0.66a5511
+          rust-typenum-1.19.0
+          rust-unicode-ident-1.0.24
+          rust-unicode-width-0.2.2
+          rust-unit-prefix-0.5.2
+          rust-url-2.5.8
+          rust-utf8-iter-1.0.4
+          rust-utf8parse-0.2.2
+          rust-vcpkg-0.2.15
+          rust-version-check-0.9.5
+          rust-voracious-radix-sort-1.2.0
+          rust-walkdir-2.5.0
+          rust-wasip2-1.0.2+wasi-0.2.9
+          rust-wasm-bindgen-0.2.118
+          rust-wasm-bindgen-macro-0.2.118
+          rust-wasm-bindgen-macro-support-0.2.118
+          rust-wasm-bindgen-shared-0.2.118
+          rust-web-sys-0.3.95
+          rust-web-time-1.1.0
+          rust-winapi-util-0.1.11
+          rust-windows-link-0.2.1
+          rust-windows-sys-0.61.2
+          rust-wit-bindgen-0.51.0
+          rust-writeable-0.6.3
+          rust-yoke-0.8.2
+          rust-yoke-derive-0.8.2
+          rust-zerocopy-0.8.48
+          rust-zerocopy-derive-0.8.48
+          rust-zerofrom-0.1.7
+          rust-zerofrom-derive-0.1.7
+          rust-zerotrie-0.2.4
+          rust-zerovec-0.11.6
+          rust-zerovec-derive-0.11.3
+          rust-zlib-rs-0.6.3
+          rust-zmij-1.0.21
+          rust-zstd-0.13.3
+          rust-zstd-safe-7.2.4
+          rust-zstd-sys-2.0.16+zstd.1.5.7)))
 
 ;;;
 ;;; Main package.
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 78b2014..5150ed9 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -45,6 +45,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages llvm)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages qt)
@@ -1293,6 +1294,116 @@ sequence data including @code{vcfeval} for variant comparison, sequence data
 simulators, and format conversion utilities.")
     (license license:bsd-2)))
 
+;; tracepoints is a library-only Rust crate (no CLI binary); its
+;; functionality is exposed via the cigzip tool below.  The crate source
+;; is available as rust-tracepoints-0.1.0.66a5511 in pangenome-rust.scm
+;; for use as a dependency.
+
+(define-public cigzip
+  (let ((commit "b7cc0ed6abb6515a8ad231d47ef90a06a3a491e8")
+        (revision "1"))
+    (package
+      (name "cigzip")
+      (version (git-version "0.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/AndreaGuarracino/cigzip")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "0kmpwkxk86428z3iva2wx0x0aavqqnx0m2sblpvw5mdd4102xjhx"))))
+      (build-system cargo-build-system)
+      (arguments
+       (list #:install-source? #f
+             ;; Tests require WFA2 C library built in OUT_DIR via build.rs
+             #:tests? #f
+             #:phases
+             #~(modify-phases %standard-phases
+                 (add-before 'build 'copy-ragc-workspace
+                   (lambda* (#:key inputs #:allow-other-keys)
+                     ;; ragc has a workspace Cargo.toml; copy it locally and
+                     ;; point dependents to the ragc-core subdir.
+                     (let ((ragc (assoc-ref inputs
+                                   "rust-ragc-core-0.1.1.40e5cad-checkout")))
+                       (copy-recursively ragc "ragc-workspace"))))
+                 (add-before 'build 'fix-dependency-sources
+                   (lambda _
+                     ;; Rewrite all git deps of cigzip and its vendored
+                     ;; transitive deps to use guix-vendor local paths.
+                     (let ((cargo-tomls
+                            (list "Cargo.toml"
+                                  "guix-vendor/rust-tpa-0.1.0.49f1801-checkout/Cargo.toml"
+                                  "guix-vendor/rust-tracepoints-0.1.0.66a5511-checkout/Cargo.toml")))
+                       (for-each
+                        (lambda (file)
+                          (when (file-exists? file)
+                            (substitute* file
+                              (("git = \"https://github.com/AndreaGuarracino/lib_wfa2\"[^,}]*(, rev = \"[0-9a-f]*\")?")
+                               "path = \"../rust-lib-wfa2-0.1.0.8859b6a-checkout\", version = \"0.1.0\"")
+                              (("git = \"https://github.com/AndreaGuarracino/tracepoints\"[^,}]*(, rev = \"[0-9a-f]*\")?")
+                               "path = \"../rust-tracepoints-0.1.0.66a5511-checkout\", version = \"0.1.0\"")
+                              (("git = \"https://github.com/AndreaGuarracino/tpa\"[^,}]*(, rev = \"[0-9a-f]*\")?")
+                               "path = \"../rust-tpa-0.1.0.49f1801-checkout\", version = \"0.1.0\"")
+                              (("git = \"https://github.com/ekg/ragc\", rev = \"40e5cad\"")
+                               "path = \"ragc-workspace/ragc-core\", version = \"0.1.1\""))))
+                        cargo-tomls)
+                       ;; The top-level Cargo.toml uses "ragc-workspace/ragc-core"
+                       ;; (relative to package root), but vendored Cargo.tomls
+                       ;; have sibling paths via ../
+                       (substitute* "Cargo.toml"
+                         (("path = \"\\.\\./rust-lib-wfa2-0.1.0.8859b6a-checkout\"")
+                          "path = \"guix-vendor/rust-lib-wfa2-0.1.0.8859b6a-checkout\"")
+                         (("path = \"\\.\\./rust-tracepoints-0.1.0.66a5511-checkout\"")
+                          "path = \"guix-vendor/rust-tracepoints-0.1.0.66a5511-checkout\"")
+                         (("path = \"\\.\\./rust-tpa-0.1.0.49f1801-checkout\"")
+                          "path = \"guix-vendor/rust-tpa-0.1.0.49f1801-checkout\"")))))
+                 (add-before 'build 'patch-lib-wfa2-use-system
+                   ;; Replace lib_wfa2 build.rs to link against system
+                   ;; wfa2-lib-static instead of building from submodule.
+                   (lambda _
+                     (let ((wfa2-build "guix-vendor/rust-lib-wfa2-0.1.0.8859b6a-checkout/build.rs"))
+                       (chmod wfa2-build #o644)
+                       (call-with-output-file wfa2-build
+                         (lambda (port)
+                           (display
+                            (string-append
+                             "fn main() {\n"
+                             "    println!(\"cargo:rustc-link-lib=static=wfa\");\n"
+                             "    println!(\"cargo:rustc-link-lib=gomp\");\n"
+                             "    println!(\"cargo:rustc-link-search=native="
+                             #$(file-append wfa2-lib-static "/lib") "\");\n"
+                             "}\n")
+                            port))))
+                     ;; Patch bindings_wfa.rs: cast_signed/cast_unsigned are
+                     ;; unstable until Rust 1.87.
+                     (substitute*
+                         "guix-vendor/rust-lib-wfa2-0.1.0.8859b6a-checkout/src/bindings_wfa.rs"
+                       (("u32::cast_signed\\(self\\._bitfield_1\\.get\\(0usize, 24u8\\) as u32\\)")
+                        "((self._bitfield_1.get(0usize, 24u8) as u32) as i32)")
+                       (("u32::cast_signed\\(<")
+                        "((<")
+                       (("            \\) as u32\\)")
+                        "            ) as u32) as i32)")
+                       (("i32::cast_unsigned\\(val\\)")
+                        "(val as u32)")
+                       (("i32::cast_unsigned\\(_flags2\\)")
+                        "(_flags2 as u32)")))))))
+      (native-inputs (list pkg-config cmake-minimal clang))
+      (inputs (cons* htslib
+                     wfa2-lib-static
+                     zlib
+                     libdeflate
+                     (list zstd "lib")
+                     (cargo-inputs 'cigzip
+                                   #:module '(gn packages pangenome-rust))))
+      (home-page "https://github.com/AndreaGuarracino/cigzip")
+      (synopsis "Compressed alignment representation using tracepoints")
+      (description "cigzip converts between CIGAR strings and tracepoint
+representations for efficient alignment storage, using adaptive tracepoints
+that segment based on local alignment complexity.")
+      (license license:expat))))
+
 (define-public gfalook
   (let ((commit "5199d77ecc4980b181177c16b94f6e56c0d06e4c")
         (revision "1"))
@@ -1371,6 +1482,7 @@ between sequences.")
      (list bandage-ng
            bedtools
            bwa-mem2
+           cigzip
            cosigt
            fastga-rs
            gafpack