[med-svn] [sumatra] 03/06: New upstream version 1.0.31
Andreas Tille
tille at debian.org
Wed Oct 18 19:31:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sumatra.
commit 8d46c1236ebf2344e1b2cf4af7831bb583eb6691
Author: Andreas Tille <tille at debian.org>
Date: Wed Oct 18 21:06:34 2017 +0200
New upstream version 1.0.31
---
._sumatra.c | Bin 0 -> 171 bytes
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
sumatra.c | 24 ++++++++++++++++++++----
79 files changed, 23 insertions(+), 4 deletions(-)
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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
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diff --git a/sumalibs/liblcs/_lcs.h b/sumalibs/liblcs/_lcs.h
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diff --git a/sumalibs/liblcs/_lcs_fast.h b/sumalibs/liblcs/_lcs_fast.h
old mode 100644
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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
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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, ¬Used, &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
old mode 100644
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diff --git a/sumalibs/liblcs/upperband.c b/sumalibs/liblcs/upperband.c
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diff --git a/sumalibs/liblcs/upperband.h b/sumalibs/liblcs/upperband.h
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diff --git a/sumalibs/libutils/utilities.c b/sumalibs/libutils/utilities.c
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diff --git a/sumalibs/libutils/utilities.h b/sumalibs/libutils/utilities.h
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diff --git a/sumatra.c b/sumatra.c
index 752ab20..7e62ca2 100644
--- a/sumatra.c
+++ b/sumatra.c
@@ -20,7 +20,7 @@
#include "./sumalibs/libutils/utilities.h"
#include "mtcompare_sumatra.h"
-#define VERSION "1.0.20"
+#define VERSION "1.0.31"
/* ----------------------------------------------- */
@@ -214,7 +214,7 @@ int compare1(fastaSeqCount db1, double threshold, BOOL normalize, int reference,
BOOL always = TRUE;
int64_t pairs = (int64_t)(db1.count - 1) * (int64_t)db1.count /2;
BOOL print;
- double score;
+ double score, scoreG;
int32_t i,j;
char* s1;
char* s2;
@@ -239,7 +239,7 @@ int compare1(fastaSeqCount db1, double threshold, BOOL normalize, int reference,
calculateMaxAndMinLenDB(db1, &lmax, &lmin);
sizeForSeqs = prepareTablesForSumathings(lmax, lmin, threshold, normalize, reference, lcsmode, &address, &iseq1, &iseq2);
- for (i=0; i < db1.count; i++) // ...??
+ for (i=0; i < db1.count; i++) // ...?? db1.count - 1 probably
for (j=i+1; j < db1.count; j++)
{
print = FALSE;
@@ -252,7 +252,23 @@ int compare1(fastaSeqCount db1, double threshold, BOOL normalize, int reference,
l1 = (db1.fastaSeqs+i)->length;
s2 = (db1.fastaSeqs+j)->sequence;
l2 = (db1.fastaSeqs+j)->length;
+
+/* fprintf(stderr, "\n%s", s1);
+ fprintf(stderr, "\n%s", s2);
+ fprintf(stderr, "\n%f", threshold);
+ fprintf(stderr, "\n%d", normalize);
+ fprintf(stderr, "\n%d", reference);
+ fprintf(stderr, "\n%d\n", lcsmode);
+*/
+// score = generic_sse_banded_lcs_align(s1, s2, threshold, normalize, reference, lcsmode);
+// fprintf(stderr, "\nscore generic = %f", scoreG);
score = alignForSumathings(s1, iseq1, s2, iseq2, l1, l2, normalize, reference, lcsmode, address, sizeForSeqs, LCSmin);
+// fprintf(stderr, "\nscore = %f\n", score);
+// if (scoreG != score)
+// {
+// fprintf(stderr, "\nscores differents\n");
+// exit(1);
+// }
print = always || (((normalize || lcsmode) && (score >= threshold)) || ((!lcsmode && !normalize) && (score <= threshold)));
if (print && !lcsmode && normalize)
score = 1.0 - score;
@@ -322,7 +338,7 @@ int compare2(fastaSeqCount db1, fastaSeqCount db2, double threshold, BOOL normal
score = alignForSumathings(s1, iseq1, s2, iseq2, l1, l2, normalize, reference, lcsmode, address, sizeForSeqs, LCSmin);
print = always || (((normalize || lcsmode) && (score >= threshold)) || ((!lcsmode && !normalize) && (score <= threshold)));
if (print && !lcsmode && normalize)
- score = 1.0 - score;
+ score = 1.0 - score; // TODO isn't that already done?
}
printResults(db1.fastaSeqs+i, db2.fastaSeqs+j, score, extradata, pairs, print);
}
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sumatra.git
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