Temporarily switching back to older bugless fasta libs while fixing a

bug
ALignment: fixed a bug where a similarity threshold of 100% would
2017-10-15 20:41:55 +02:00 · 2017-10-13 18:55:30 +02:00 · 2017-10-13 18:54:17 +02:00
36 changed files with 3 additions and 0 deletions
--- a/Licence_CeCILL_V2-en.txt
+++ b/Licence_CeCILL_V2-en.txt
--- a/Licence_CeCILL_V2-fr.txt
+++ b/Licence_CeCILL_V2-fr.txt
--- a/global.mk
+++ b/global.mk
--- a/libfasta/Makefile
+++ b/libfasta/Makefile
--- a/libfasta/fasta_header_handler.c
+++ b/libfasta/fasta_header_handler.c
--- a/libfasta/fasta_header_handler.h
+++ b/libfasta/fasta_header_handler.h
--- a/libfasta/fasta_header_parser.c
+++ b/libfasta/fasta_header_parser.c
--- a/libfasta/fasta_header_parser.h
+++ b/libfasta/fasta_header_parser.h
--- a/libfasta/fasta_header_parser.l
+++ b/libfasta/fasta_header_parser.l
--- a/libfasta/fasta_seq_writer.c
+++ b/libfasta/fasta_seq_writer.c
--- a/libfasta/fasta_seq_writer.h
+++ b/libfasta/fasta_seq_writer.h
--- a/libfasta/header_mem_handler.c
+++ b/libfasta/header_mem_handler.c
--- a/libfasta/header_mem_handler.h
+++ b/libfasta/header_mem_handler.h
--- a/libfasta/sequence.c
+++ b/libfasta/sequence.c
--- a/libfasta/sequence.h
+++ b/libfasta/sequence.h
--- a/libfile/Makefile
+++ b/libfile/Makefile
--- a/libfile/fileHandling.c
+++ b/libfile/fileHandling.c
--- a/libfile/fileHandling.h
+++ b/libfile/fileHandling.h
--- a/liblcs/Makefile
+++ b/liblcs/Makefile
--- a/liblcs/_lcs.ext.1.c
+++ b/liblcs/_lcs.ext.1.c
--- a/liblcs/_lcs.ext.2.c
+++ b/liblcs/_lcs.ext.2.c
--- a/liblcs/_lcs.ext.3.c
+++ b/liblcs/_lcs.ext.3.c
--- a/liblcs/_lcs.h
+++ b/liblcs/_lcs.h
--- a/liblcs/_lcs_fast.h
+++ b/liblcs/_lcs_fast.h
--- a/liblcs/banded_LCS_alignment.c
+++ b/liblcs/banded_LCS_alignment.c
--- a/liblcs/banded_LCS_alignment.h
+++ b/liblcs/banded_LCS_alignment.h
--- a/liblcs/sse_banded_LCS_alignment.c
+++ b/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;
--- a/liblcs/sse_banded_LCS_alignment.h
+++ b/liblcs/sse_banded_LCS_alignment.h
--- a/liblcs/upperband.c
+++ b/liblcs/upperband.c
--- a/liblcs/upperband.h
+++ b/liblcs/upperband.h
--- a/libsse/_sse.h
+++ b/libsse/_sse.h
--- a/libutils/Makefile
+++ b/libutils/Makefile
--- a/libutils/debug.c
+++ b/libutils/debug.c
--- a/libutils/debug.h
+++ b/libutils/debug.h
--- a/libutils/utilities.c
+++ b/libutils/utilities.c
--- a/libutils/utilities.h
+++ b/libutils/utilities.h
Author	SHA1	Message	Date
Celine Mercier	6373bc1c20	Temporarily switching back to older bugless fasta libs while fixing a bug	2017-10-15 20:41:55 +02:00
Celine Mercier	f9d0ac00aa	ALignment: fixed a bug where a similarity threshold of 100% would generate memory bugs	2017-10-13 18:55:30 +02:00
Celine Mercier	a258d334b1	Improved the fasta parser for better memory handling and better parsing of the last parts of fasta headers (definitions)	2017-10-13 18:54:17 +02:00