[med-svn] r21800 - in trunk/packages/seqprep/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Apr 28 18:52:17 UTC 2016
Author: tille
Date: 2016-04-28 18:52:15 +0000 (Thu, 28 Apr 2016)
New Revision: 21800
Modified:
trunk/packages/seqprep/trunk/debian/changelog
trunk/packages/seqprep/trunk/debian/control
trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch
trunk/packages/seqprep/trunk/debian/patches/hardening.patch
trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch
Log:
New upstream version
Modified: trunk/packages/seqprep/trunk/debian/changelog
===================================================================
--- trunk/packages/seqprep/trunk/debian/changelog 2016-04-28 10:38:34 UTC (rev 21799)
+++ trunk/packages/seqprep/trunk/debian/changelog 2016-04-28 18:52:15 UTC (rev 21800)
@@ -1,3 +1,9 @@
+seqprep (1.2-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Apr 2016 20:36:22 +0200
+
seqprep (1.1-6) unstable; urgency=medium
* Add missing Python dependency to tests (Thanks for the patch to
Modified: trunk/packages/seqprep/trunk/debian/control
===================================================================
--- trunk/packages/seqprep/trunk/debian/control 2016-04-28 10:38:34 UTC (rev 21799)
+++ trunk/packages/seqprep/trunk/debian/control 2016-04-28 18:52:15 UTC (rev 21800)
@@ -9,7 +9,7 @@
python-markdown,
ruby-ronn,
zlib1g-dev
-Standards-Version: 3.9.7
+Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/seqprep/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seqprep/trunk/
Homepage: http://seqanswers.com/wiki/SeqPrep
Modified: trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch 2016-04-28 10:38:34 UTC (rev 21799)
+++ trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch 2016-04-28 18:52:15 UTC (rev 21800)
@@ -5,8 +5,8 @@
--- a/SeqPrep.c
+++ b/SeqPrep.c
-@@ -67,7 +67,7 @@
- fprintf(stderr, "\t-X <read alignment maximum fraction gap cutoff; default = %f>\n", DEF_READ_GAP_FRAC_CUTOFF );
+@@ -68,7 +68,7 @@ void help ( char *prog_name ) {
+ fprintf(stderr, "\t-z <use mask; N will replace adapters>\n");
fprintf(stderr, "Optional Arguments for Merging:\n" );
fprintf(stderr, "\t-y <maximum quality score in output ((phred 33) default = '%c' )>\n", maximum_quality );
- fprintf(stderr, "\t-g <print overhang when adapters are present and stripped (use this if reads are different length)>\n");
@@ -14,16 +14,16 @@
fprintf(stderr, "\t-s <perform merging and output the merged reads to this file>\n" );
fprintf(stderr, "\t-E <write pretty alignments to this file for visual Examination>\n" );
fprintf(stderr, "\t-x <max number of pretty alignments to write (if -E provided); default = %d>\n", DEF_MAX_PRETTY_PRINT );
-@@ -133,7 +133,7 @@
+@@ -120,7 +120,7 @@ int main( int argc, char* argv[] ) {
char reverse_discard_fn[MAX_FN_LEN];
char merged_out_fn[MAX_FN_LEN];
bool do_read_merging = false;
- bool print_overhang = false;
+// bool print_overhang = false;
bool write_discard=false;
+ bool use_mask=false;
char forward_primer[MAX_SEQ_LEN+1];
- strcpy(forward_primer, DEF_FORWARD_PRIMER); //set default
-@@ -270,7 +270,8 @@
+@@ -261,7 +261,8 @@ int main( int argc, char* argv[] ) {
maximum_quality = optarg[0];
break;
case 'g' :
@@ -35,7 +35,7 @@
do_read_merging = true;
--- a/stdaln.c
+++ b/stdaln.c
-@@ -545,13 +545,12 @@
+@@ -545,13 +545,12 @@ int aln_local_core(unsigned char *seq1,
int start, end, max_score;
int thres, *suba, *ss;
@@ -50,7 +50,7 @@
score_matrix = ap->matrix;
N_MATRIX_ROW = ap->row;
thres = _thres > 0? _thres : -_thres;
-@@ -865,7 +864,7 @@
+@@ -865,7 +864,7 @@ uint16_t *aln_path2cigar(const path_t *p
int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
path_t *path, int *path_len, int G0, uint8_t *_mem)
{
@@ -59,7 +59,7 @@
int32_t **s_array, *score_array;
int is_overflow, of_base;
uint32_t *eh;
-@@ -892,7 +891,6 @@
+@@ -892,7 +891,6 @@ int aln_extend_core(unsigned char *seq1,
s_array[i] = (int32_t*)_p, _p += 4 * len1;
/* initialization */
aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
Modified: trunk/packages/seqprep/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/hardening.patch 2016-04-28 10:38:34 UTC (rev 21799)
+++ trunk/packages/seqprep/trunk/debian/patches/hardening.patch 2016-04-28 18:52:15 UTC (rev 21800)
@@ -4,10 +4,9 @@
--- a/Makefile
+++ b/Makefile
-@@ -1,8 +1,8 @@
- CC=gcc
--CFLAGS=-c -Wall -Werror -O0 -g
-+CFLAGS+=-c -Wall -Werror -O0 -g
+@@ -1,7 +1,7 @@
+-CFLAGS=-c -Wall -O0 -g -std=c99
++CFLAGS+=-c -Wall -O0 -g -std=c99
#recommended options: -ffast-math -ftree-vectorize -march=core2 -mssse3 -O3
COPTS=
-LDFLAGS=-lz -lm
Modified: trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch 2016-04-28 10:38:34 UTC (rev 21799)
+++ trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch 2016-04-28 18:52:15 UTC (rev 21800)
@@ -5,7 +5,7 @@
--- a/SeqPrep.c
+++ b/SeqPrep.c
-@@ -150,12 +150,12 @@
+@@ -138,12 +138,12 @@ int main( int argc, char* argv[] ) {
int min_ol_adapter = DEF_OL2MERGE_ADAPTER;
int min_ol_reads = DEF_OL2MERGE_READS;
unsigned short int min_read_len =DEF_MIN_READ_LEN;
@@ -23,7 +23,7 @@
unsigned short max_mismatch_adapter[MAX_SEQ_LEN+1];
unsigned short max_mismatch_reads[MAX_SEQ_LEN+1];
unsigned short min_match_adapter[MAX_SEQ_LEN+1];
-@@ -316,10 +316,10 @@
+@@ -307,10 +307,10 @@ int main( int argc, char* argv[] ) {
//Calculate table matching overlap length to min matches and max mismatches
for(i=0;i<MAX_SEQ_LEN+1;i++){
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