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commit f12a8dc000316f974a4a5b86876782d6946634dc Author: Andreas Tille <[email protected]> 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 <[email protected]>. # @@ -745,8 +745,8 @@ SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='Clustal Omega' PACKAGE_TARNAME='clustal-omega' -PACKAGE_VERSION='1.2.2' -PACKAGE_STRING='Clustal Omega 1.2.2' +PACKAGE_VERSION='1.2.3' +PACKAGE_STRING='Clustal Omega 1.2.3' PACKAGE_BUGREPORT='[email protected]' # Factoring default headers for most tests. @@ -1483,7 +1483,7 @@ if test "$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 = $CONFIG_FILES @@ -21853,7 +21853,7 @@ Report bugs to <[email protected]>." _ACEOF cat >>$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], [[email protected]]) #PACKAGE_CODENAME="AndreaGiacomo" -AC_INIT([Clustal Omega], [1.2.2], [[email protected]]) +# r310 +#AC_INIT([Clustal Omega], [1.2.2], [[email protected]]) +#PACKAGE_CODENAME="AndreaGiacomo" +# r313 +AC_INIT([Clustal Omega], [1.2.3], [[email protected]]) 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; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/clustalo.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
