Kalign version 3.3.1

TimoLassmann · Apr 16, 2021 · 1d0bfe3 · 1d0bfe3
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,25 @@
+2021-04-16  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+
+	* version 3.3.1 - Bug Fix
+	The previous version kalign checked the top 50 sequences in inputs to determine
+	whether the sequences are aligned or not. If the first 50 sequences are not aligned,
+	but following sequences contain gaps (or other characters!) kalign can crash. In this
+	version (3.3.1) kalign checks all sequences, thereby avoiding this issue.
+	To alert users to the situation described above and to warn users about the presence of
+	odd characters, kalign now produces a warning message like this:
+
+	[Date Time] :     LOG : Start io tests.
+	[Date Time] :     LOG : reading: dev/data/a2m.good.1
+	[Date Time] :     LOG : Detected protein sequences.
+	[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 505)
+	[Date Time] : WARNING : The input sequences contain gap characters:  (rwalign.c line 506)
+	[Date Time] : WARNING : "-" :   36 found                             (rwalign.c line 510)
+	[Date Time] : WARNING : BUT the sequences do not seem to be aligned! (rwalign.c line 514)
+	[Date Time] : WARNING :                                              (rwalign.c line 515)
+	[Date Time] : WARNING : Kalign will remove the gap characters and    (rwalign.c line 516)
+	[Date Time] : WARNING : align the sequences.                         (rwalign.c line 517)
+	[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 518)
+
 2020-11-06  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
 
 	* version 3.3 - Threading and more

diff --git a/README b/README
@@ -1,48 +1,106 @@
 -----------------------------------------------------------------------
-  Kalign version 2.03, Copyright (C) 2006 Timo Lassmann
-
-  http://msa.cgb.ki.se/
-  timolassmann@gmail.com
-
-	This program is free software; you can redistribute it and/or modify
-	it under the terms of the GNU General Public License as published by
-	the Free Software Foundation; either version 2 of the License, or
-	any later version.
-
-	This program is distributed in the hope that it will be useful,
-	but WITHOUT ANY WARRANTY; without even the implied warranty of
-	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-	GNU General Public License for more details.
-
-	You should have received a copy of the GNU General Public License
-	along with this program; if not, write to the Free Software
-	Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-	A copy of this license is in the COPYING file.
+    Kalign - a multiple sequence alignment program
+
+    Copyright 2006, 2019, 2020, 2021 Timo Lassmann
+
+    This file is part of kalign.
+
+    Kalign is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 -----------------------------------------------------------------------
-Installation:
 
-% ./configure 
-% make
+Kalign is a fast multiple sequence alignment program for biological sequences.
+
+1) Installation
+
+1.1) Release Tarball
+
+Download tarball from [releases](https://github.com/TimoLassmann/kalign/releases). Then:
+
+tar -zxvf kalign-<version>.tar.gz
+cd kalign-<version>
+./autogen.sh
+./configure
+make
+make check
+make install
+
+
+1.2) Homebrew
+
+brew install brewsci/bio/kalign
+
+1.3) Developer version
+
+git clone https://github.com/TimoLassmann/kalign.git
+cd kalign
+./autogen.sh
+./configure
+make
+make check
+make install
+
+
+1.4) on macOS, install [brew](https://brew.sh/) then:
+
+brew install libtool
+brew install automake
+git clone https://github.com/TimoLassmann/kalign.git
+cd kalign
+./autogen.sh
+./configure
+make
+make check
+make install
+
+
+2) Usage
+
+Usage: kalign  -i <seq file> -o <out aln>
+
+Options:
+
+   --format           : Output format. [Fasta]
+   --reformat         : Reformat existing alignment. [NA]
+   --version          : Print version and exit
+
+Kalign expects the input to be a set of unaligned sequences in fasta format or aligned sequences in aligned fasta, MSF or clustal format. Kalign automatically detects whether the input sequences are protein, RNA or DNA.
+
+Since version 3.2.0 kalign supports passing sequence in via stdin and support alignment of sequences from multiple files.
+
+3) Examples
+
+Passing sequences via stdin:
+
+   cat input.fa | kalign -f fasta > out.afa
+
+Combining multiple input files:
+
+   kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa
+
+Align sequences and output the alignment in MSF format:
+
+   kalign -i BB11001.tfa -f msf  -o out.msf
 
-and as root:
+Align sequences and output the alignment in clustal format:
 
-% make install
+   kalign -i BB11001.tfa -f clu -o out.clu
 
+Re-align sequences in an existing alignment:
 
-Usage:
+   kalign -i BB11001.msf  -o out.afa
 
-        kalign [Options]  infile.fasta outfile.fasta
-
-        or:
-
-        kalign [Options] -i infile.fasta -o outfile.fasta
-
-        or:
-
-        kalign [Options] < infile.fasta > outfile.fasta
+Reformat existing alignment:
 
-        Options:
-
-	type: kalign -h 
-
+   kalign -i BB11001.msf -r afa -o out.afa
diff --git a/configure.ac b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT(kalign, 3.3)
+AC_INIT(kalign, 3.3.1)
 
 #AC_CONFIG_AUX_DIR([.])
 

diff --git a/dev/run_io_test.sh b/dev/run_io_test.sh
@@ -18,5 +18,4 @@ do
         printf "with ERROR $status and Message:\n\n$error\n\n";
         exit 1;
     fi
-
 done
diff --git a/src/alignment_parameters.c b/src/alignment_parameters.c
@@ -30,7 +30,7 @@ int set_param_number(struct aln_param* ap,int L, int sel);
 
 int new_aln_matrices(struct aln_param* ap);
 
-int init_ap(struct aln_param** aln_param, struct parameters* param, int numseq,int L)
+int init_ap(struct aln_param** aln_param, struct parameters* param,int L)
 {
         struct aln_param* ap = NULL;
         int i,j;

diff --git a/src/alignment_parameters.h b/src/alignment_parameters.h
@@ -55,6 +55,6 @@ struct aln_param{
 
 };
 
-extern int init_ap(struct aln_param** aln_param, struct parameters* param, int numseq,int L);
+extern int init_ap(struct aln_param** aln_param, struct parameters* param,int L);
 extern void free_ap(struct aln_param* ap);
 #endif
diff --git a/src/aln_run.c b/src/aln_run.c
@@ -868,6 +868,7 @@ int do_align_serial(struct msa* msa,struct aln_tasks* t,struct aln_mem* m, int t
         MFREE(t->profile[b]);
 
         t->profile[c] = tmp;
+
         RUN(make_seq(msa,a,b,m->path));
 
         msa->plen[c] = m->path[0];

diff --git a/src/run_kalign.c b/src/run_kalign.c
@@ -1,7 +1,7 @@
 /*
     Kalign - a multiple sequence alignment program
 
-    Copyright 2006, 2019, 2020 Timo Lassmann
+    Copyright 2006, 2019, 2020, 2021 Timo Lassmann
 
     This file is part of kalign.
 
@@ -132,7 +132,7 @@ int print_kalign_header(void)
         fprintf(stdout,"\n");
         fprintf(stdout,"Kalign (%s)\n", PACKAGE_VERSION);
         fprintf(stdout,"\n");
-        fprintf(stdout,"Copyright (C) 2006,2019,2020 Timo Lassmann\n");
+        fprintf(stdout,"Copyright (C) 2006,2019,2020,2021 Timo Lassmann\n");
         fprintf(stdout,"\n");
         fprintf(stdout,"This program comes with ABSOLUTELY NO WARRANTY; for details type:\n");
         fprintf(stdout,"`kalign -showw'.\n");
@@ -520,7 +520,7 @@ int run_kalign(struct parameters* param)
         }
 
         /* allocate aln parameters  */
-        RUN(init_ap(&ap,param,msa->numseq,msa->L ));
+        RUN(init_ap(&ap,param,msa->L ));
 
         if(param->dump_internal){
                 double* s;
@@ -555,7 +555,7 @@ int run_kalign(struct parameters* param)
                 RUN(convert_msa_to_internal(msa, ALPHA_ambigiousPROTEIN));
         }
         /* allocate aln parameters  */
-        RUN(init_ap(&ap,param,msa->numseq,msa->L ));
+        RUN(init_ap(&ap,param,msa->L ));
 
         /* Start alignment stuff */
         DECLARE_TIMER(t1);
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,5 +18,4 @@ do @@
             printf "with ERROR $status and Message:\n\n$error\n\n";
             exit 1;
         fi
     done