M gnu/local.mk => gnu/local.mk +0 -1
@@ 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 \
M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +0 -12
@@ 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")
D gnu/packages/patches/htslib-for-stringtie.patch => gnu/packages/patches/htslib-for-stringtie.patch +0 -26
@@ 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