9966f98b1b
* 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.
26 lines
1 KiB
Diff
26 lines
1 KiB
Diff
These changes are commits d7e357946ead219b81cc1becbe0de8a99d96ca84 and
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8ed0daa39bc662defa99507f926815431056543a in
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https://github.com/samtools/htscodecs. The stringtie package expects these
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changes to have been applied.
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diff -ru htslib-1.12/htscodecs/htscodecs/tokenise_name3.c stringtie-2.2.0/htslib/htscodecs/htscodecs/tokenise_name3.c
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--- a/htscodecs/htscodecs/tokenise_name3.c 2021-02-22 13:07:06.000000000 +0100
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+++ b/htscodecs/htscodecs/tokenise_name3.c 2021-12-04 19:27:39.000000000 +0100
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@@ -211,7 +211,7 @@
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if (!ctx) return NULL;
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ctx->max_names = max_names;
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pthread_setspecific(tok_key, ctx);
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- } else if (ctx->max_names < max_names) {
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+ } else if (ctx->max_names < max_names+1) {
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ctx = realloc(ctx, sizeof(*ctx) + ++max_names*sizeof(*ctx->lc));
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if (!ctx) return NULL;
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ctx->max_names = max_names;
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@@ -1058,6 +1058,8 @@
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tok = decode_token_type(ctx, ntok);
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//fprintf(stderr, "Tok %d = %d\n", ntok, tok);
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+ ctx->lc[cnum].last_ntok = 0;
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+
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switch (tok) {
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case N_CHAR:
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if (len+1 >= name_len) return -1;
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