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Diffstat (limited to 'sci-biology/meme/files/meme-4.11.2_p2-patch2.patch')
| -rw-r--r-- | sci-biology/meme/files/meme-4.11.2_p2-patch2.patch | 54 |
1 files changed, 0 insertions, 54 deletions
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch deleted file mode 100644 index 498d1df7b664..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- a/doc/release-notes.html -+++ b/doc/release-notes.html -@@ -15,6 +15,21 @@ - </div> - <h2>MEME Suite Release Notes</h2> - <hr> -+ <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b> -+ <ul> -+ <li> -+ <b>Bug fixes</b> -+ <ul> -+ <li> -+ Fixed bug in handling of RNA-like custom alphabets. -+ </li> -+ <li> -+ Fixed bug in MAST -comp option. -+ </li> -+ </ul -+ </li> -+ </ul> -+ <hr> - <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b> - <ul> - <li> ---- a/src/alph-in.c -+++ b/src/alph-in.c -@@ -1044,7 +1044,7 @@ - lookup[0] = sym->complement; - comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup); - } -- if (comp1 != comp2) { -+ if (comp1 && (comp1 != comp2)) { - add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, - "not like %s alphabet as %c complement rules are incorrect", - ext_name, req_syms[i])); ---- a/src/mast-util.c -+++ b/src/mast-util.c -@@ -740,14 +740,14 @@ - - // create the frequency array - alph = xlate ? xlate_dest_alph(xlate) : alph; -- freq = allocate_array(alph_size_core(alph)); -+ freq = allocate_array(alph_size_full(alph)); - init_array(0, freq); - - // count the number of letters of each type - if (xlate) { - for (n=0; sequence[n]; n++) { - i = xlate_index(xlate, false, sequence+n); -- if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq); -+ if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq); - } - } else { - for (n=0; sequence[n]; n++) { |