[med-svn] [sumaclust] 03/06: New upstream version 1.0.31

Andreas Tille tille at debian.org
Wed Oct 18 18:16:19 UTC 2017 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sumaclust.

commit a62dd4a13b7708eeba3aa09c199b4932560dedc2
Author: Andreas Tille <tille at debian.org>
Date:   Wed Oct 18 20:04:59 2017 +0200

    New upstream version 1.0.31
---
 ._sumaclust.c                                | Bin 0 -> 171 bytes
 sumaclust.c                                  |   7 +++----
 sumalibs/._Licence_CeCILL_V2-en.txt          | Bin 0 -> 226 bytes
 sumalibs/._Licence_CeCILL_V2-fr.txt          | Bin 0 -> 226 bytes
 sumalibs/._global.mk                         | Bin 171 -> 226 bytes
 sumalibs/._libfasta                          | Bin 0 -> 226 bytes
 sumalibs/._libfile                           | Bin 0 -> 226 bytes
 sumalibs/._liblcs                            | Bin 0 -> 226 bytes
 sumalibs/._libsse                            | Bin 0 -> 226 bytes
 sumalibs/._libutils                          | Bin 0 -> 226 bytes
 sumalibs/Licence_CeCILL_V2-en.txt            |   0
 sumalibs/Licence_CeCILL_V2-fr.txt            |   0
 sumalibs/global.mk                           |   0
 sumalibs/libfasta/._Makefile                 | Bin 171 -> 226 bytes
 sumalibs/libfasta/._fasta_header_handler.c   | Bin 0 -> 226 bytes
 sumalibs/libfasta/._fasta_header_handler.h   | Bin 0 -> 226 bytes
 sumalibs/libfasta/._fasta_header_parser.c    | Bin 0 -> 226 bytes
 sumalibs/libfasta/._fasta_header_parser.h    | Bin 0 -> 226 bytes
 sumalibs/libfasta/._fasta_header_parser.l    | Bin 0 -> 226 bytes
 sumalibs/libfasta/._fasta_seq_writer.c       | Bin 0 -> 226 bytes
 sumalibs/libfasta/._fasta_seq_writer.h       | Bin 0 -> 226 bytes
 sumalibs/libfasta/._header_mem_handler.c     | Bin 0 -> 226 bytes
 sumalibs/libfasta/._header_mem_handler.h     | Bin 0 -> 226 bytes
 sumalibs/libfasta/._sequence.c               | Bin 0 -> 226 bytes
 sumalibs/libfasta/._sequence.h               | Bin 0 -> 226 bytes
 sumalibs/libfasta/Makefile                   |   0
 sumalibs/libfasta/fasta_header_handler.c     |   0
 sumalibs/libfasta/fasta_header_handler.h     |   0
 sumalibs/libfasta/fasta_header_parser.c      |   0
 sumalibs/libfasta/fasta_header_parser.h      |   0
 sumalibs/libfasta/fasta_header_parser.l      |   0
 sumalibs/libfasta/fasta_seq_writer.c         |   0
 sumalibs/libfasta/fasta_seq_writer.h         |   0
 sumalibs/libfasta/header_mem_handler.c       |   0
 sumalibs/libfasta/header_mem_handler.h       |   0
 sumalibs/libfasta/sequence.c                 |   0
 sumalibs/libfasta/sequence.h                 |   0
 sumalibs/libfile/._Makefile                  | Bin 171 -> 226 bytes
 sumalibs/libfile/._fileHandling.c            | Bin 0 -> 226 bytes
 sumalibs/libfile/._fileHandling.h            | Bin 0 -> 226 bytes
 sumalibs/libfile/Makefile                    |   0
 sumalibs/libfile/fileHandling.c              |   0
 sumalibs/libfile/fileHandling.h              |   0
 sumalibs/liblcs/._Makefile                   | Bin 171 -> 226 bytes
 sumalibs/liblcs/.__lcs.ext.1.c               | Bin 0 -> 226 bytes
 sumalibs/liblcs/.__lcs.ext.2.c               | Bin 0 -> 226 bytes
 sumalibs/liblcs/.__lcs.ext.3.c               | Bin 0 -> 226 bytes
 sumalibs/liblcs/.__lcs.h                     | Bin 0 -> 226 bytes
 sumalibs/liblcs/.__lcs_fast.h                | Bin 0 -> 226 bytes
 sumalibs/liblcs/._banded_LCS_alignment.c     | Bin 0 -> 226 bytes
 sumalibs/liblcs/._banded_LCS_alignment.h     | Bin 0 -> 226 bytes
 sumalibs/liblcs/._sse_banded_LCS_alignment.c | Bin 0 -> 226 bytes
 sumalibs/liblcs/._sse_banded_LCS_alignment.h | Bin 0 -> 226 bytes
 sumalibs/liblcs/._upperband.c                | Bin 0 -> 226 bytes
 sumalibs/liblcs/._upperband.h                | Bin 0 -> 226 bytes
 sumalibs/liblcs/Makefile                     |   0
 sumalibs/liblcs/_lcs.ext.1.c                 |   0
 sumalibs/liblcs/_lcs.ext.2.c                 |   0
 sumalibs/liblcs/_lcs.ext.3.c                 |   0
 sumalibs/liblcs/_lcs.h                       |   0
 sumalibs/liblcs/_lcs_fast.h                  |   0
 sumalibs/liblcs/banded_LCS_alignment.c       |   0
 sumalibs/liblcs/banded_LCS_alignment.h       |   0
 sumalibs/liblcs/sse_banded_LCS_alignment.c   |   3 +++
 sumalibs/liblcs/sse_banded_LCS_alignment.h   |   0
 sumalibs/liblcs/upperband.c                  |   0
 sumalibs/liblcs/upperband.h                  |   0
 sumalibs/libsse/.__sse.h                     | Bin 0 -> 226 bytes
 sumalibs/libsse/_sse.h                       |   0
 sumalibs/libutils/._Makefile                 | Bin 171 -> 226 bytes
 sumalibs/libutils/._debug.c                  | Bin 0 -> 226 bytes
 sumalibs/libutils/._debug.h                  | Bin 0 -> 226 bytes
 sumalibs/libutils/._utilities.c              | Bin 0 -> 226 bytes
 sumalibs/libutils/._utilities.h              | Bin 0 -> 226 bytes
 sumalibs/libutils/Makefile                   |   0
 sumalibs/libutils/debug.c                    |   0
 sumalibs/libutils/debug.h                    |   0
 sumalibs/libutils/utilities.c                |   0
 sumalibs/libutils/utilities.h                |   0
 79 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/._sumaclust.c b/._sumaclust.c
new file mode 100644
index 0000000..cd621b2
Binary files /dev/null and b/._sumaclust.c differ
diff --git a/sumaclust.c b/sumaclust.c
index e3e9e49..df0e778 100644
--- a/sumaclust.c
+++ b/sumaclust.c
@@ -23,7 +23,7 @@
 #include "mtcompare_sumaclust.h"
 #include "sumaclust.h"
 
-#define VERSION "1.0.20"
+#define VERSION "1.0.31"
 
 
 /* ----------------------------------------------- */
@@ -585,7 +585,7 @@ void putSeqInCluster(fastaSeqPtr* seq, fastaSeqPtr* center, double score)
 }
 
 
-int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
+int compare(fastaSeqPtr* db, int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
 		double max_ratio)
 {
 	double       score;
@@ -723,7 +723,7 @@ int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL nor
 	free(iseq1-sizeForSeqs+lmax);
 	free(iseq2-sizeForSeqs+lmax);
 
-	if (normalize && reference == ALILEN)
+	if (normalize && (reference == ALILEN))
 		free(address);
 
 	return(k);
@@ -1037,7 +1037,6 @@ int main(int argc, char** argv)
 	// FASTA file
 	if (printFASTA)
 	{
-
 		if (printFASTAtofile)
 		{
 			FASTA_output = fopen(FASTA_file_name, "w");
diff --git a/sumalibs/._Licence_CeCILL_V2-en.txt b/sumalibs/._Licence_CeCILL_V2-en.txt
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diff --git a/sumalibs/._libfile b/sumalibs/._libfile
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diff --git a/sumalibs/._libsse b/sumalibs/._libsse
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diff --git a/sumalibs/global.mk b/sumalibs/global.mk
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diff --git a/sumalibs/libfasta/sequence.c b/sumalibs/libfasta/sequence.c
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diff --git a/sumalibs/liblcs/Makefile b/sumalibs/liblcs/Makefile
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diff --git a/sumalibs/liblcs/_lcs.ext.1.c b/sumalibs/liblcs/_lcs.ext.1.c
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diff --git a/sumalibs/liblcs/_lcs.ext.2.c b/sumalibs/liblcs/_lcs.ext.2.c
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diff --git a/sumalibs/liblcs/_lcs.ext.3.c b/sumalibs/liblcs/_lcs.ext.3.c
old mode 100644
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diff --git a/sumalibs/liblcs/_lcs.h b/sumalibs/liblcs/_lcs.h
old mode 100644
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diff --git a/sumalibs/liblcs/_lcs_fast.h b/sumalibs/liblcs/_lcs_fast.h
old mode 100644
new mode 100755
diff --git a/sumalibs/liblcs/banded_LCS_alignment.c b/sumalibs/liblcs/banded_LCS_alignment.c
old mode 100644
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diff --git a/sumalibs/liblcs/banded_LCS_alignment.h b/sumalibs/liblcs/banded_LCS_alignment.h
old mode 100644
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diff --git a/sumalibs/liblcs/sse_banded_LCS_alignment.c b/sumalibs/liblcs/sse_banded_LCS_alignment.c
old mode 100644
new mode 100755
index 425c6f7..c254aea
--- a/sumalibs/liblcs/sse_banded_LCS_alignment.c
+++ b/sumalibs/liblcs/sse_banded_LCS_alignment.c
@@ -458,6 +458,9 @@ int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin)
 
 	calculateBandLengths(maxLen, minLen, &notUsed, &size, LCSmin);		// max size = max left band length * 2
 
+	if (!size)	// Happens if there is no threshold (threshold is 100% similarity) and generates bugs if left to 0
+		size = 1;
+
 	//fprintf(stderr, "\nsize for address before %8 = %d", size);
 
 	size*= 2;
diff --git a/sumalibs/liblcs/sse_banded_LCS_alignment.h b/sumalibs/liblcs/sse_banded_LCS_alignment.h
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