[med-svn] r20149 - in trunk/packages/seqprep/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon Sep 28 06:24:35 UTC 2015
Author: tille
Date: 2015-09-28 06:24:34 +0000 (Mon, 28 Sep 2015)
New Revision: 20149
Added:
trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch
trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch
Removed:
trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors
Modified:
trunk/packages/seqprep/trunk/debian/changelog
trunk/packages/seqprep/trunk/debian/patches/series
trunk/packages/seqprep/trunk/debian/rules
Log:
Commit changes by Graham Inggs
Modified: trunk/packages/seqprep/trunk/debian/changelog
===================================================================
--- trunk/packages/seqprep/trunk/debian/changelog 2015-09-27 06:13:23 UTC (rev 20148)
+++ trunk/packages/seqprep/trunk/debian/changelog 2015-09-28 06:24:34 UTC (rev 20149)
@@ -1,6 +1,13 @@
seqprep (1.1-3) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* make sure autopkgtest script will not fail when cleaning up
+
+ [ Graham Inggs ]
+ * enable building with gcc-5
+ * fix clean target
+ * replace all instances of the 'float' datatype in SeqPrep.c with 'double'
+ Closes: #789829
-- Andreas Tille <tille at debian.org> Tue, 07 Jul 2015 09:45:10 +0200
Deleted: trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors 2015-09-27 06:13:23 UTC (rev 20148)
+++ trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors 2015-09-28 06:24:34 UTC (rev 20149)
@@ -1,69 +0,0 @@
-Author: Tim Booth <tbooth at ceh.ac.uk>
-Last-Update: Thu, 19 Feb 2015 16:49:55 +0000
-Description: Default Debian compiler options throw errors for
- unused variables. This patch is removing those variables.
-
---- 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 );
- 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");
-+ fprintf(stderr, "\t-g <print overhang when adapters are present and stripped (use this if reads are different length)> - UNIMPLEMENTED\n");
- 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 @@
- 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;
- char forward_primer[MAX_SEQ_LEN+1];
- strcpy(forward_primer, DEF_FORWARD_PRIMER); //set default
-@@ -270,7 +270,8 @@
- maximum_quality = optarg[0];
- break;
- case 'g' :
-- print_overhang = true;
-+ //print_overhang is never used!
-+ //print_overhang = true;
- break;
- case 's' :
- do_read_merging = true;
---- a/stdaln.c
-+++ b/stdaln.c
-@@ -545,13 +545,12 @@
- int start, end, max_score;
- int thres, *suba, *ss;
-
-- int gap_open, gap_ext, b;
-+ int gap_open, gap_ext;
- int *score_matrix, N_MATRIX_ROW;
-
- /* initialize some align-related parameters. just for compatibility */
- gap_open = ap->gap_open;
- gap_ext = ap->gap_ext;
-- b = ap->band_width;
- score_matrix = ap->matrix;
- N_MATRIX_ROW = ap->row;
- thres = _thres > 0? _thres : -_thres;
-@@ -865,7 +864,7 @@
- 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)
- {
-- int q, r, qr, tmp_len;
-+ int q, r, qr;
- int32_t **s_array, *score_array;
- int is_overflow, of_base;
- uint32_t *eh;
-@@ -892,7 +891,6 @@
- s_array[i] = (int32_t*)_p, _p += 4 * len1;
- /* initialization */
- aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
-- tmp_len = len1 + 1;
- start = 1; end = 2;
- end_i = end_j = 0;
- score = 0;
Added: trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch (rev 0)
+++ trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch 2015-09-28 06:24:34 UTC (rev 20149)
@@ -0,0 +1,69 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Thu, 19 Feb 2015 16:49:55 +0000
+Description: Default Debian compiler options throw errors for
+ unused variables. This patch is removing those variables.
+
+--- 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 );
+ 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");
++ fprintf(stderr, "\t-g <print overhang when adapters are present and stripped (use this if reads are different length)> - UNIMPLEMENTED\n");
+ 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 @@
+ 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;
+ char forward_primer[MAX_SEQ_LEN+1];
+ strcpy(forward_primer, DEF_FORWARD_PRIMER); //set default
+@@ -270,7 +270,8 @@
+ maximum_quality = optarg[0];
+ break;
+ case 'g' :
+- print_overhang = true;
++ //print_overhang is never used!
++ //print_overhang = true;
+ break;
+ case 's' :
+ do_read_merging = true;
+--- a/stdaln.c
++++ b/stdaln.c
+@@ -545,13 +545,12 @@
+ int start, end, max_score;
+ int thres, *suba, *ss;
+
+- int gap_open, gap_ext, b;
++ int gap_open, gap_ext;
+ int *score_matrix, N_MATRIX_ROW;
+
+ /* initialize some align-related parameters. just for compatibility */
+ gap_open = ap->gap_open;
+ gap_ext = ap->gap_ext;
+- b = ap->band_width;
+ score_matrix = ap->matrix;
+ N_MATRIX_ROW = ap->row;
+ thres = _thres > 0? _thres : -_thres;
+@@ -865,7 +864,7 @@
+ 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)
+ {
+- int q, r, qr, tmp_len;
++ int q, r, qr;
+ int32_t **s_array, *score_array;
+ int is_overflow, of_base;
+ uint32_t *eh;
+@@ -892,7 +891,6 @@
+ s_array[i] = (int32_t*)_p, _p += 4 * len1;
+ /* initialization */
+ aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
+- tmp_len = len1 + 1;
+ start = 1; end = 2;
+ end_i = end_j = 0;
+ score = 0;
Added: trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch (rev 0)
+++ trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch 2015-09-28 06:24:34 UTC (rev 20149)
@@ -0,0 +1,40 @@
+Author: Graham Inggs <ginggs at debian.org>
+Last-Update: Sun, 27 Sep 2015 11:52:43 +0200
+Bug-Debian: http://bugs.debian.org/789829
+Description: replace all instances of the 'float' datatype in SeqPrep.c with 'double'
+
+--- a/SeqPrep.c
++++ b/SeqPrep.c
+@@ -150,12 +150,12 @@
+ int min_ol_adapter = DEF_OL2MERGE_ADAPTER;
+ int min_ol_reads = DEF_OL2MERGE_READS;
+ unsigned short int min_read_len =DEF_MIN_READ_LEN;
+- float min_match_adapter_frac = DEF_MIN_MATCH_ADAPTER;
+- float min_match_reads_frac = DEF_MIN_MATCH_READS;
+- float max_mismatch_adapter_frac = DEF_MAX_MISMATCH_ADAPTER;
+- float max_mismatch_reads_frac = DEF_MAX_MISMATCH_READS;
++ double min_match_adapter_frac = DEF_MIN_MATCH_ADAPTER;
++ double min_match_reads_frac = DEF_MIN_MATCH_READS;
++ double max_mismatch_adapter_frac = DEF_MAX_MISMATCH_ADAPTER;
++ double max_mismatch_reads_frac = DEF_MAX_MISMATCH_READS;
+
+- float read_frac_thresh = DEF_READ_GAP_FRAC_CUTOFF;
++ double read_frac_thresh = DEF_READ_GAP_FRAC_CUTOFF;
+ 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 @@
+
+ //Calculate table matching overlap length to min matches and max mismatches
+ for(i=0;i<MAX_SEQ_LEN+1;i++){
+- max_mismatch_reads[i] = floor(((float)i)*max_mismatch_reads_frac);
+- max_mismatch_adapter[i] = floor(((float)i)*max_mismatch_adapter_frac);
+- min_match_reads[i] = ceil(((float)i)*min_match_reads_frac);
+- min_match_adapter[i] = ceil(((float)i)*min_match_adapter_frac);
++ max_mismatch_reads[i] = floor(((double)i)*max_mismatch_reads_frac);
++ max_mismatch_adapter[i] = floor(((double)i)*max_mismatch_adapter_frac);
++ min_match_reads[i] = ceil(((double)i)*min_match_reads_frac);
++ min_match_adapter[i] = ceil(((double)i)*min_match_adapter_frac);
+ }
+ //get length of forward and reverse primers
+ int forward_primer_len = strlen(forward_primer);
Modified: trunk/packages/seqprep/trunk/debian/patches/series
===================================================================
--- trunk/packages/seqprep/trunk/debian/patches/series 2015-09-27 06:13:23 UTC (rev 20148)
+++ trunk/packages/seqprep/trunk/debian/patches/series 2015-09-28 06:24:34 UTC (rev 20149)
@@ -1,2 +1,3 @@
-fix_unused_variable_errors
+fix_unused_variable_errors.patch
hardening.patch
+# replace-float-with-double.patch
Modified: trunk/packages/seqprep/trunk/debian/rules
===================================================================
--- trunk/packages/seqprep/trunk/debian/rules 2015-09-27 06:13:23 UTC (rev 20148)
+++ trunk/packages/seqprep/trunk/debian/rules 2015-09-28 06:24:34 UTC (rev 20149)
@@ -1,6 +1,8 @@
#!/usr/bin/make -f
#export DH_VERBOSE=1
+export DEB_CFLAGS_MAINT_APPEND=-std=gnu90
+
%:
dh $@
@@ -14,6 +16,7 @@
dh_clean
rm -f seqprep
rm -f debian/*.1
+ rm -f README.html
override_dh_auto_test:
# This checks that the tests run and produce byte-identical results.
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