From 9966f98b1b4e17b8a80865ad1e1938aff703bdfe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 11 Jan 2022 14:15:04 +0100
Subject: gnu: Add htslib-for-stringtie.

* gnu/packages/bioinformatics.scm (htslib-for-stringtie): New variable.
* gnu/packages/patches/htslib-for-stringtie.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                    |  1 +
 gnu/packages/bioinformatics.scm                 | 12 ++++++++++++
 gnu/packages/patches/htslib-for-stringtie.patch | 26 +++++++++++++++++++++++++
 3 files changed, 39 insertions(+)
 create mode 100644 gnu/packages/patches/htslib-for-stringtie.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index e4f596f0bd..feadac4bad 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1255,6 +1255,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/hedgewars-network-bsd.patch		\
   %D%/packages/patches/helm-fix-gcc-9-build.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/hurd-cross.patch				\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 487c43a2da..2b9a27d44b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4884,6 +4884,18 @@ data.  It also provides the @command{bgzip}, @command{htsfile}, and
     (native-inputs
      `(("perl" ,perl)))))
 
+(define htslib-for-stringtie
+  (package
+    (inherit htslib)
+    (source (origin
+              (inherit (package-source htslib))
+              (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
new file mode 100644
index 0000000000..3e6cd5bb63
--- /dev/null
+++ b/gnu/packages/patches/htslib-for-stringtie.patch
@@ -0,0 +1,26 @@
+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
-- 
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