T2GD 1.19.1 "Shenlong"

T2GD 1.19.1 "Shenlong"

A build-recipe release. It is built from the same source tree as 1.19.0
"Shenlong" (2026-07-31) and produces the same records; what changed is how the
binaries are compiled.

T2GD converts alignments made against a transcriptome FASTA into genome
coordinates, using a GTF annotation as the map, and ships 36 subcommands around
that core operation. See CHANGELOG.md for what is in the
release and INSTALL.md for how to install it.

If you are running 1.19.0, nothing here requires you to change anything.
There is no source change, no change to the command line surface, and no change
to any record T2GD writes. Upgrade if you want the speed.

What is new in 1.19.1

Link time optimisation is removed from the five shipping
release recipes: release-znver4, release-znver2, release-broadwell,
release-apple and release-generic. That is the whole change.

What you may notice

• The @PG VN: field moves from 1.19.0-Shenlong to 1.19.1-Shenlong. This
  is the only difference in a BAM header, and it does not affect records. Two
  BAMs converted by 1.19.0 and 1.19.1 will not be byte-identical for that reason
  their record streams are.
• Binary size moves, and not in the same direction on both platforms.

Binary	1.19.0	1.19.1	Change
linux-broadwell/t2gd	12,372,728	9,927,464	-19.8%
linux-broadwell/t2gd-cli	5,495,096	3,778,888	-31.2%
macos-arm64/t2gd	7,252,432	13,208,960	+82.1%
macos-arm64/t2gd-cli	3,445,248	4,491,744	+30.4%

Artifacts

Platform	Archive	Size	Binaries
Linux x86_64, znver4	t2gd-1.19.1-Shenlong-linux-x86_64-znver4.tar.gz	4,290,601	t2gd, t2gd-cli
Linux x86_64, znver2	t2gd-1.19.1-Shenlong-linux-x86_64-znver2.tar.gz	4,237,374	t2gd, t2gd-cli
Linux x86_64, broadwell	t2gd-1.19.1-Shenlong-linux-x86_64-broadwell.tar.gz	4,248,488	t2gd, t2gd-cli
macOS arm64	t2gd-1.19.1-Shenlong-macos-arm64.tar.gz	8,559,092	T2GD.app, t2gd, t2gd-cli
Windows x86_64	t2gd-1.19.1-Shenlong-windows-x86_64.zip	27,172,265	t2gd.exe, t2gd-cli.exe
Windows x86_64, installer	t2gd-1.19.1-Shenlong-windows-x86_64-setup.exe	19,599,036	t2gd.exe, t2gd-cli.exe

Which one. If you are unsure, take broadwell; it runs everywhere the
other two Linux builds do. znver4 needs AVX-512, so AMD Zen 4 or newer.
znver2 needs AMD Zen 2 or newer. The macOS build is Apple Silicon only and
needs macOS 14 or newer. The Windows build runs on any x86-64 machine with
Windows 10 or newer.

Which binary. t2gd is the full build and runs headless as
t2gd --cli <subcommand>. t2gd-cli contains no graphical code at all and is
the binary to use on HPC nodes and in containers. On macOS, use t2gd-cli for
command line work: the full binary looks for GTK at startup and macOS has no
system-wide search path that finds a Homebrew install.

Windows ships the same pair, t2gd.exe and t2gd-cli.exe.

Checksums

SHA-256 of the release archives. These are also in SHA256SUMS alongside the
archives.

e823155f9823501577d93da1085576cc935e6d7c66557ea81f3b981a8288e0ec  t2gd-1.19.1-Shenlong-linux-x86_64-znver4.tar.gz
c8b0728ae50c584b1bc1c196207c925d985f4d20b0ca2a8feb0b33aaec9a0744  t2gd-1.19.1-Shenlong-linux-x86_64-znver2.tar.gz
cb0a5dd8ae7dd5fcbd780e93da887eff325a67fb32b18ab7f43a37644e34c318  t2gd-1.19.1-Shenlong-linux-x86_64-broadwell.tar.gz
e6b97dc27102353bea3509a951a6a85ecb094da2f415511a5a698b4902ae5499  t2gd-1.19.1-Shenlong-macos-arm64.tar.gz
ed940aa2f6d6dfc5f2c7497e55188a2c810fbd1784c860c8876d37141f064b71  t2gd-1.19.1-Shenlong-windows-x86_64.zip
671d6b5489819a8d1e45e6f81512863426032312c0b9ff7f2130cb9973860c58  t2gd-1.19.1-Shenlong-windows-x86_64-setup.exe

Verify a download:

sha256sum -c SHA256SUMS --ignore-missing

On macOS, shasum -a 256 -c SHA256SUMS --ignore-missing. On Windows,
certutil -hashfile t2gd-1.19.1-Shenlong-windows-x86_64.zip SHA256.

SHA-256 of the executables themselves, after unpacking. Each archive also
carries its own SHA256SUMS, which you can check from inside the unpacked
folder.

a1a5a6318f76ce382faf95c2d5c192d736c00e9877d0d7230ab33ba222010c06  linux-znver4/t2gd
7cb22fc9d60b9dba26a2f0f9b25c84b6958b38e45a467e9da5dcd460eb296218  linux-znver4/t2gd-cli
9e3ece76a7babfbfc3bd263ae153b73a06bda21cd6969d2f54e9a1bb0343188b  linux-znver2/t2gd
951d37452987dbc7d726db48178adf152c5679c62d5f1df8f2b10741bb0d9b2d  linux-znver2/t2gd-cli
f2283770d19b8f5d9a55eedfa4ff093408234ce108fe09e5f52f36cce007c7ed  linux-broadwell/t2gd
5f50fe5820f4842414d573efd25704368cb32cdef1ee5f000c9f3c1820aa0a22  linux-broadwell/t2gd-cli
0f169318f00068c800e975d1b5ef78715880ca7946edea9acafc9fa90c11ade6  macos-arm64/t2gd
af8ed5651b504641cdf93df6f7d62788eb053acebd10a17887d86514936badf7  macos-arm64/t2gd-cli
9c70c063740e38af9fdd612f8469c6289c51fa11e170ce9ca515d53e8dacfaa3  macos-arm64/T2GD.app/Contents/MacOS/T2GD
5a47b56f73e0915d59adfc1388e3ebc67b88ec01904e957279d62963a7e63750  macos-arm64/T2GD.app/Contents/MacOS/t2gd-bin
f86dcab12fc41c0b3b3263eee28f949551ad8e821973c63c8304b474861faaeb  windows-x64/t2gd.exe
3d473667b47d41a89cfa6ed0a3debb853eacf978ab14e90a4fddaa388eff5a74  windows-x64/t2gd-cli.exe

What is in each archive

Every archive contains the binaries, plus:

File	What it is
README.md	Start here. What the tool is and the one command that runs it.
CHANGELOG.md	What is in this release.
LICENSE.txt	CC BY-NC-ND 4.0, with a plain-language summary.
RUN_LINUX.txt, RUN_MACOS.txt or RUN_WINDOWS.txt	Platform-specific first-run notes.
SHA256SUMS	Checksums for the binaries and the documents listed above.

SHA256SUMS covers the executables and the four documents. On Windows it does
not cover the bundled GTK runtime, which is 910 further files; those are
covered by the checksum of the archive as a whole.

The Windows archive additionally carries that runtime: 47 DLLs beside
t2gd.exe, the gdk-pixbuf loaders under lib\ (17 files), and themes and
icons under share\ (846 files), 917 files in the archive altogether. Nothing
needs installing and no environment variable is required, because Windows
searches the executable's own directory first. t2gd-cli.exe needs none of it
and runs on its own.

The macOS archive additionally carries T2GD.app. Open that rather than
double-clicking the bare t2gd: Finder hands a bare executable to Terminal,
so the bundle is what makes the interface open without one.

The manual is inside the executable. Nothing is fetched at runtime and nothing
is installed alongside, so t2gd help works on a machine with no network.

Dependencies

None beyond the platform system libraries. The D runtime and libdeflate are
linked in. Removing LTO does not change this; the link record is identical to
1.19.0 on every platform.

On Linux, readelf -d NEEDED lists only libz, libm, libgcc_s, libc and
ld-linux — verified on all six Linux binaries in this release. On macOS,
otool -L lists only libz, libSystem and libobjc, all from /usr/lib,
with no Homebrew path baked in and no LC_RPATH. On Windows the import table
lists only KERNEL32.dll, ADVAPI32.dll and WS2_32.dll.

GTK 3 is absent from the link record on every platform, including in the full
build, because the toolkit is loaded at startup rather than linked. That is a
runtime load, not a weak link, so the full binary still needs GTK present at
startup even when you run it as t2gd --cli. The binary that needs no GTK at
all is t2gd-cli, which contains no graphical code.

Determinism across platforms

Every platform produces the same records from the same input. This is verified
on each release by comparing the record stream checksum of the same conversion
run on each build. A result therefore does not change when you move machines.

Because 1.19.1 changes no conversion code, the record stream it produces must
match 1.19.0 and 1.18.0 exactly.

Build provenance

Item	Linux	macOS arm64	Windows x86_64
Compiler	LDC 1.42.0 (DMD v2.112.1, LLVM 21.1.8)	LDC 1.42.0 (DMD v2.112.1, LLVM 21.1.8)	LDC 1.40.0 (DMD v2.110.0, LLVM 19.1.3)
Platform toolchain	GNU ld, glibc	Apple clang 21.0.0, macOS 26.2	MSVC 19.50.35726 x64
Build type	release-znver4, release-znver2, release-broadwell	release-apple	release (dub built-in)
LTO	none	none	none, and never was
GTK 3	not linked, loaded at runtime	3.24.52, loaded at runtime	3.24.51, bundled and loaded at runtime

The binaries are not code-signed. On macOS, clear the quarantine attribute
after unpacking with xattr -dr com.apple.quarantine <folder>. On Windows,
SmartScreen will warn on first run; choose More info then Run anyway.
Both are consequences of an unsigned download, not of anything the binary does.

The Windows installer is unsigned for the same reason, and it will draw a
louder SmartScreen warning than the zip does, because it asks for elevation and
offers to edit PATH. That combination is exactly the shape SmartScreen is
built to object to. If that is not a trade you want to make, use the zip: it
contains the same files and needs no elevation at all.

Known limitations

• The znver4 build was not executed before release.
• The Installing T2GD topic built into the executable still gives its example
  filenames as t2gd-1.19.0-....
• The manual built into the executable carries a screenshot of every tab, and
  two of those pictures are stale, unchanged from 1.19.0.
• The 1.18.0 section of CHANGELOG.md opens "The first public
  release". That was written before the decision not to distribute Fafnir, and
  it is wrong: 1.19.0 was the first release to leave the building.
• There is no Intel Mac build and no universal binary.
• Below roughly 4 GB of memory, a human-sized annotation will not fit however
  the run is configured.

Licence

The binaries, the bundled documentation and the Python reference implementation
under python/ are all licensed under CC BY-NC-ND 4.0. The
NoDerivatives term applies to the Python source too: it is published to be read,
run and cited, not forked. The T2GD D source tree is not covered by this licence
and is not distributed here. For commercial licensing, see https://biocodecs.org.

Note that python/ is in the repository, not in these archives. The five
release archives contain the binary and its documentation only.

Copyright (c) 2026 Biocodecs, Arnaroo Ribologicals, COMPASS.