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| author | Ricardo Wurmus <rekado@elephly.net> | 2022-01-11 14:15:04 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-01-11 14:19:53 +0100 |
| commit | 9966f98b1b4e17b8a80865ad1e1938aff703bdfe (patch) | |
| tree | 1fa995781b6d5f2dd6bd0f5b1de495e41d589520 /gnu/packages/patches | |
| parent | 5b200dbfb0714016b3731ef288b7821f30ec2524 (diff) | |
| download | guix-patches-9966f98b1b4e17b8a80865ad1e1938aff703bdfe.tar guix-patches-9966f98b1b4e17b8a80865ad1e1938aff703bdfe.tar.gz | |
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.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/htslib-for-stringtie.patch | 26 |
1 files changed, 26 insertions, 0 deletions
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;
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