[med-svn] [clustalo] 01/04: Imported Upstream version 1.2.3
Andreas Tille
tille at debian.org
Tue Aug 30 06:46:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository clustalo.
commit f12a8dc000316f974a4a5b86876782d6946634dc
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 30 08:25:01 2016 +0200
Imported Upstream version 1.2.3
---
ChangeLog | 76 +++++++++++++++++++++++++++++++++++++++++++---
Doxyfile | 2 +-
configure | 20 ++++++------
configure.ac | 8 +++--
src/clustal-omega-config.h | 6 ++--
src/squid/clustal.c | 6 ++--
6 files changed, 94 insertions(+), 24 deletions(-)
diff --git a/ChangeLog b/ChangeLog
old mode 100644
new mode 100755
index 49114b6..ed8e870
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,13 +1,69 @@
-2012-04-25 Release 1.1.0
+2016-07-20 Release 1.2.3 (AndreaGiacomo, r313)
+
+ - fixed consensus line in ClustalW format, 'H' in NHQK not recognised as strong (bug in Squid)
+
+ (no new command-line flags)
+
+2016-07-01 Release 1.2.2 (AndreaGiacomo, r310)
+
+ - fixed a memory leak in hhalign
+ - parallelised hhalign
+ - increased MAC-RAM default from 2GB to 8GB
+
+ (no new command-line flags)
+
+2014-02-28 Release 1.2.1 (AndreaGiacomo, r292)
+
+ - corrected Clustal format consensus line
+ - label justification (multi-bit)
+
+2013-06-12 Release 1.2.0 (AndreaGiacomo, r284)
+
+ --is-profile disable check if profile, force profile (default no)
+ --use-kimura use Kimura distance correction for aligned sequences (default no)
+ --percent-id convert distances into percent identities (default no)
+
+ fixed bug in --output-order=tree-order for pair-wise alignment
+
+ Kimura distance correction no longer default for protein
+
+ fixed bug in Viterbi algorithm (predominantly affected long nucleotide but also protein, to lesser extent)
+
+ Viterbi is less (~10x) memory hungry than MAC but still scales quadratically with length:
+
+ 2GB of RAM (ClustalO default) can align sequences of 6.5k residues with MAC and 18k with Viterbi
+
+ 8GB of RAM (EBI limit) can align sequences of 12.5k residues with MAC and 37k with Viterbi
+
+ A Viterbi alignment of sequences of 100k residues will require 59GB of RAM
+
+
+2013-05-16 Release 1.1.1 (r281)
+
+ --cluster-size=<n> soft maximum of sequences in sub-clusters
+ --clustering-out=<file> Clustering output file
+ --residuenumber, --resno in Clustal format print residue numbers (default no)
+ --wrap=<n> number of residues before line-wrap in output
+ --output-order={input-order,tree-order} MSA output order like in input/guide-tree
+
+ turned off Kimura correction for DNA/RNA
+
+ enable distance matrix output after initial mBed but subsequent full distance calculation
+
+ enable termination after distance/guide-tree calculation (--max-hmm-iterations=-1)
+
+ longer sequence labels
+
+2012-04-25 Release 1.1.0 (FilumVitae, r275)
DNA and RNA support now added. Sequence type can be specified manually
using --seqtype={Protein|DNA|RNA}
-2012-03-27 Release 1.0.4
+2012-03-27 Release 1.0.4 (r273)
zipped input now supported
-2011-09-07 Release 1.0.3
+2011-09-07 Release 1.0.3 (r263)
Bugs fixed:
@@ -27,11 +83,21 @@ Bugs fixed:
doxygen documentation fixes and fix of API example
+ introduced MAC-RAM flag to set amount of RAM given to MAC (in MB)
+
2011-06-23 Release 1.0.2
-2011-06-17 Release 1.0.0 (DeshilHollesEamus)
+2011-06-17 Release 1.0.0 (DeshilHollesEamus, r250)
+
+2011-04-14 Release 0.2.0 (IbiMeVidebunt, r238)
-2010-06-17 Release 0.0.1 (Dubliniensis)
+2011-03-23 Release 0.1.1 (OppidumLeonis, r224)
+
+2011-02-22 Release 0.1.0 (OppidumLeonis, r200)
+
+2010-08-10 Release 0.0.3 (Thamesis, r120)
+
+2010-06-17 Release 0.0.1 (Dubliniensis, r81)
First "release" as program has been able for a while to perform
all basic tasks without problems.
diff --git a/Doxyfile b/Doxyfile
index 0c9b5c9..cde71e7 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -31,7 +31,7 @@ PROJECT_NAME = "Clustal Omega"
# This could be handy for archiving the generated documentation or
# if some version control system is used.
-PROJECT_NUMBER = 1.2.2
+PROJECT_NUMBER = 1.2.3
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
# base path where the generated documentation will be put.
diff --git a/configure b/configure
index b2a728b..3090f0a 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.63 for Clustal Omega 1.2.2.
+# Generated by GNU Autoconf 2.63 for Clustal Omega 1.2.3.
#
# Report bugs to <clustalw at ucd.ie>.
#
@@ -745,8 +745,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='Clustal Omega'
PACKAGE_TARNAME='clustal-omega'
-PACKAGE_VERSION='1.2.2'
-PACKAGE_STRING='Clustal Omega 1.2.2'
+PACKAGE_VERSION='1.2.3'
+PACKAGE_STRING='Clustal Omega 1.2.3'
PACKAGE_BUGREPORT='clustalw at ucd.ie'
# Factoring default headers for most tests.
@@ -1483,7 +1483,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures Clustal Omega 1.2.2 to adapt to many kinds of systems.
+\`configure' configures Clustal Omega 1.2.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1553,7 +1553,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of Clustal Omega 1.2.2:";;
+ short | recursive ) echo "Configuration of Clustal Omega 1.2.3:";;
esac
cat <<\_ACEOF
@@ -1659,7 +1659,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-Clustal Omega configure 1.2.2
+Clustal Omega configure 1.2.3
generated by GNU Autoconf 2.63
Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -1673,7 +1673,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by Clustal Omega $as_me 1.2.2, which was
+It was created by Clustal Omega $as_me 1.2.3, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ $0 $@
@@ -2492,7 +2492,7 @@ fi
# Define the identity of the package.
PACKAGE='clustal-omega'
- VERSION='1.2.2'
+ VERSION='1.2.3'
cat >>confdefs.h <<_ACEOF
@@ -21790,7 +21790,7 @@ exec 6>&1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by Clustal Omega $as_me 1.2.2, which was
+This file was extended by Clustal Omega $as_me 1.2.3, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -21853,7 +21853,7 @@ Report bugs to <bug-autoconf at gnu.org>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_version="\\
-Clustal Omega config.status 1.2.2
+Clustal Omega config.status 1.2.3
configured by $0, generated by GNU Autoconf 2.63,
with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
diff --git a/configure.ac b/configure.ac
index aa10e17..d827cf8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,6 +1,6 @@
# configure.ac for Clustal Omega
#
-# RCS $Id: configure.ac 310 2016-06-13 14:11:35Z fabian $
+# RCS $Id: configure.ac 313 2016-07-20 13:30:29Z fabian $
# release
@@ -28,7 +28,11 @@
#PACKAGE_CODENAME="AndreaGiacomo"
#AC_INIT([Clustal Omega], [1.2.1], [clustalw at ucd.ie])
#PACKAGE_CODENAME="AndreaGiacomo"
-AC_INIT([Clustal Omega], [1.2.2], [clustalw at ucd.ie])
+# r310
+#AC_INIT([Clustal Omega], [1.2.2], [clustalw at ucd.ie])
+#PACKAGE_CODENAME="AndreaGiacomo"
+# r313
+AC_INIT([Clustal Omega], [1.2.3], [clustalw at ucd.ie])
PACKAGE_CODENAME="AndreaGiacomo"
# The AC_INIT macro can take any source file as an argument. It just
diff --git a/src/clustal-omega-config.h b/src/clustal-omega-config.h
index ba86373..edcbc4b 100644
--- a/src/clustal-omega-config.h
+++ b/src/clustal-omega-config.h
@@ -228,7 +228,7 @@
/* Define to the full name and version of this package. */
#ifndef CLUSTAL_OMEGA_PACKAGE_STRING
-#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.2.2"
+#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.2.3"
#endif
/* Define to the one symbol short name of this package. */
@@ -238,7 +238,7 @@
/* Define to the version of this package. */
#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION
-#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.2.2"
+#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.2.3"
#endif
/* The size of `fpos_t', as computed by sizeof. */
@@ -301,7 +301,7 @@
/* Version number of package */
#ifndef CLUSTAL_OMEGA_VERSION
-#define CLUSTAL_OMEGA_VERSION "1.2.2"
+#define CLUSTAL_OMEGA_VERSION "1.2.3"
#endif
/* Define if using the dmalloc debugging malloc package */
diff --git a/src/squid/clustal.c b/src/squid/clustal.c
index f928ea0..06f5400 100644
--- a/src/squid/clustal.c
+++ b/src/squid/clustal.c
@@ -14,7 +14,7 @@
* formatted files. Derivative of msf.c; MSF is a pretty
* generic interleaved format.
*
- * RCS $Id: clustal.c 291 2014-02-27 18:20:54Z fabian $ (Original squid RCS Id: clustal.c,v 1.1 1999/07/15 22:26:53 eddy Exp)
+ * RCS $Id: clustal.c 312 2016-07-14 16:57:39Z fabian $ (Original squid RCS Id: clustal.c,v 1.1 1999/07/15 22:26:53 eddy Exp)
*/
#include <stdbool.h>
@@ -343,7 +343,7 @@ WriteClustal(FILE *fp, MSA *msa)
case 'K': strong_bins[1]++; strong_bins[2]++; strong_bins[4]++; break;
case 'D': strong_bins[3]++; break;
case 'R': strong_bins[4]++; break;
- case 'H': strong_bins[4]++; strong_bins[7]++; break;
+ case 'H': strong_bins[2]++; strong_bins[4]++; strong_bins[7]++; break; /* added bin-2 (NHQK), FS 2016-07-14 */
case 'M': strong_bins[5]++; strong_bins[6]++; break;
case 'I': strong_bins[5]++; strong_bins[6]++; break;
case 'L': strong_bins[5]++; strong_bins[6]++; break;
@@ -377,7 +377,7 @@ WriteClustal(FILE *fp, MSA *msa)
case 'A': weak_bins[0]++; weak_bins[1]++; weak_bins[2]++; weak_bins[4]++; break;
case 'T': weak_bins[1]++; weak_bins[3]++; weak_bins[4]++; break;
case 'V': weak_bins[1]++; weak_bins[9]++; break;
- case 'G': weak_bins[2]++; break;
+ case 'G': weak_bins[2]++; weak_bins[5]++; break; /* Added bin-5, FS 2016-07-14 */
case 'N': weak_bins[3]++; weak_bins[5]++; weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
case 'K': weak_bins[3]++; weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
case 'D': weak_bins[5]++; weak_bins[6]++; weak_bins[7]++; break;
--
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