From d8352498fb5c74f09a2bfcfa5c169180e8caaddf Mon Sep 17 00:00:00 2001
From: cryptogenomicon <sean@eddylab.org>
Date: Mon, 29 Feb 2016 12:02:49 -0500
Subject: [PATCH] One p7_oprofile_Clone() call updated to p7_oprofile_Shadow(),
 following API change in hmmer.

'make tags' changed to call a new makeTAGS.sh script instead.  By
running ./makeTAGS.sh directly, you can use tag searching without
needing to ./configure a Makefile. In my src/, I now create a
supertags file for HMMER, Easel, and Infernal, so I can easily search
all our Easel- or HMMER-dependent code when I'm changing something in
an API (like p7_oprofile_Clone() getting renamed).
---
 Makefile.in    |  9 +++------
 makeTAGS.sh    | 15 +++++++++++++++
 src/cmsearch.c |  2 +-
 3 files changed, 19 insertions(+), 7 deletions(-)
 create mode 100755 makeTAGS.sh

diff --git a/Makefile.in b/Makefile.in
index 87772566..e59c9929 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -227,10 +227,7 @@ distclean:
 
 # "make TAGS": emacs etags database, for searching the whole source tree.
 TAGS:
-	etags    src/*.[ch]        src/*.in
-	etags -a testsuite/*.[ch]  testsuite/*.in
-	etags -a easel/*.[ch]      easel/*.in
+	./makeTAGS.sh
+
+
 
-################################################################
-# @LICENSE@
-################################################################
diff --git a/makeTAGS.sh b/makeTAGS.sh
new file mode 100755
index 00000000..b8020d7f
--- /dev/null
+++ b/makeTAGS.sh
@@ -0,0 +1,15 @@
+#! /bin/sh
+
+etags    configure.ac
+etags -a INSTALL
+etags -a LICENSE
+
+# Recursively add all .c, .h, .pl, *.tex, *.man
+find . -name "*.c"   -print -or -name "*.h"  -print | xargs etags -a
+find . -name "*.pl"  -print -or -name "*.pm" -print | xargs etags -a
+find . -name "*.sh"  -print                         | xargs etags -a
+find . -name "*.tex" -print                         | xargs etags -a
+find . -name "*.man" -print                         | xargs etags -a
+find . -name "*.in"  -print                         | xargs etags -a
+find . -name "*.sqc" -print                         | xargs etags -a
+find . -name "*README"    -print                    | xargs etags -a
diff --git a/src/cmsearch.c b/src/cmsearch.c
index f47e295b..b324ec0d 100644
--- a/src/cmsearch.c
+++ b/src/cmsearch.c
@@ -2328,7 +2328,7 @@ clone_info(ESL_GETOPTS *go, WORKER_INFO *src_info, WORKER_INFO *dest_infoA, int
     if(src_info->Rgm != NULL) { if((dest_infoA[i].Rgm = p7_profile_Clone(src_info->Rgm)) == NULL) goto ERROR; }
     if(src_info->Lgm != NULL) { if((dest_infoA[i].Lgm = p7_profile_Clone(src_info->Lgm)) == NULL) goto ERROR; }
     if(src_info->Tgm != NULL) { if((dest_infoA[i].Tgm = p7_profile_Clone(src_info->Tgm)) == NULL) goto ERROR; }
-    if((dest_infoA[i].om  = p7_oprofile_Clone(src_info->om)) == NULL) goto ERROR;
+    if((dest_infoA[i].om  = p7_oprofile_Shadow(src_info->om)) == NULL) goto ERROR;
     if((dest_infoA[i].bg  = p7_bg_Create(src_info->bg->abc)) == NULL) goto ERROR;
     if(dest_infoA[i].p7_evparam == NULL) ESL_ALLOC(dest_infoA[i].p7_evparam, sizeof(float) * CM_p7_NEVPARAM);
     esl_vec_FCopy(src_info->cm->fp7_evparam, CM_p7_NEVPARAM, dest_infoA[i].p7_evparam);