From ff6b3eb2794264dbc6e81289da53d36881d60e8c Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 23 Oct 2025 21:41:34 +0200
Subject: [PATCH] gnu: Remove htslib-for-stringtie.

* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Delete variable.
* gnu/packages/patches/htslib-for-stringtie.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.

Change-Id: Idbf3fa982895baed97913e08650cbff6947e8182
---
 gnu/local.mk                                  |  1 -
 gnu/packages/bioinformatics.scm               | 12 ---------
 .../patches/htslib-for-stringtie.patch        | 26 -------------------
 3 files changed, 39 deletions(-)
 delete mode 100644 gnu/packages/patches/htslib-for-stringtie.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 7601067a8466bce8001bb9eaf13a5aafdab87b22..2d059f3535bd6efe48881ce2a9926692607bb161 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1574,7 +1574,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/highlight-gui-data-dir.patch		\
   %D%/packages/patches/hplip-usb-timeout.patch			\
   %D%/packages/patches/http-parser-CVE-2020-8287.patch		\
-  %D%/packages/patches/htslib-for-stringtie.patch		\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hueplusplus-mbedtls.patch		\
   %D%/packages/patches/hugs-fix-build.patch			\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c726dcf376d06753bead0492a06dd710a9010dee..8951d3377b55f7c6e7d90fd3aa05eb48a02941e3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9662,18 +9662,6 @@ data.  It also provides the @command{bgzip}, @command{htsfile}, and
                (base32
                 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
 
-(define htslib-for-stringtie
-  (package
-    (inherit htslib-1.12)
-    (source (origin
-              (inherit (package-source htslib-1.12))
-              (patches
-               (search-patches "htslib-for-stringtie.patch"))))
-    (arguments
-     `(#:configure-flags '("--with-libdeflate")))
-    (inputs
-     (list bzip2 libdeflate openssl))))
-
 (define-public idr
   (package
     (name "idr")
diff --git a/gnu/packages/patches/htslib-for-stringtie.patch b/gnu/packages/patches/htslib-for-stringtie.patch
deleted file mode 100644
index 3e6cd5bb63edff12edc5e28153c623c16d0b12ce..0000000000000000000000000000000000000000
--- a/gnu/packages/patches/htslib-for-stringtie.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-These changes are commits d7e357946ead219b81cc1becbe0de8a99d96ca84 and
-8ed0daa39bc662defa99507f926815431056543a in
-https://github.com/samtools/htscodecs.  The stringtie package expects these
-changes to have been applied.
-
-diff -ru htslib-1.12/htscodecs/htscodecs/tokenise_name3.c stringtie-2.2.0/htslib/htscodecs/htscodecs/tokenise_name3.c
---- a/htscodecs/htscodecs/tokenise_name3.c	2021-02-22 13:07:06.000000000 +0100
-+++ b/htscodecs/htscodecs/tokenise_name3.c	2021-12-04 19:27:39.000000000 +0100
-@@ -211,7 +211,7 @@
- 	if (!ctx) return NULL;
- 	ctx->max_names = max_names;
- 	pthread_setspecific(tok_key, ctx);
--    } else if (ctx->max_names < max_names) {
-+    } else if (ctx->max_names < max_names+1) {
- 	ctx = realloc(ctx, sizeof(*ctx) + ++max_names*sizeof(*ctx->lc));
- 	if (!ctx) return NULL;
- 	ctx->max_names = max_names;
-@@ -1058,6 +1058,8 @@
- 	tok = decode_token_type(ctx, ntok);
- 	//fprintf(stderr, "Tok %d = %d\n", ntok, tok);
- 
-+	ctx->lc[cnum].last_ntok = 0;
-+
- 	switch (tok) {
- 	case N_CHAR:
- 	    if (len+1 >= name_len) return -1;
\ No newline at end of file