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gnu: Add htslib-for-stringtie.

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* 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.
This commit is contained in:
Ricardo Wurmus 2022-01-11 14:15:04 +01:00
parent 5b200dbfb0
commit 9966f98b1b
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3 changed files with 39 additions and 0 deletions
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26
gnu/packages/patches/htslib-for-stringtie.patch Normal file
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@ -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;