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path: root/gnu/packages/patches/htslib-for-stringtie.patch
blob: 3e6cd5bb63edff12edc5e28153c623c16d0b12ce (plain) (blame)
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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;